SMTL ID : 4ci0.1 (2 other biounits)

Electron cryo-microscopy of F420-reducing NiFe hydrogenase Frh

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.36 Å

Oligo State

hetero-12-12-12-mer

Ligands

12 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: C.66, A.326, V.349, P.350, C.383 Ligands: NI.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.66, A:C.383 FE.10: 6 residues within 4Å: Chain D: C.66, A.326, V.349, P.350, C.383 Ligands: NI.11 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.66, D:C.383 FE.19: 6 residues within 4Å: Chain G: C.66, A.326, V.349, P.350, C.383 Ligands: NI.20 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:C.66, G:C.383 FE.28: 6 residues within 4Å: Chain J: C.66, A.326, V.349, P.350, C.383 Ligands: NI.29 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:C.66, J:C.383 FE.37: 6 residues within 4Å: Chain M: C.66, A.326, V.349, P.350, C.383 Ligands: NI.38 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:C.66, M:C.383 FE.46: 6 residues within 4Å: Chain P: C.66, A.326, V.349, P.350, C.383 Ligands: NI.47 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:C.66, P:C.383 FE.55: 6 residues within 4Å: Chain S: C.66, A.326, V.349, P.350, C.383 Ligands: NI.56 2 PLIP interactions: 2 interactions with chain S Metal complexes: S:C.66, S:C.383 FE.64: 6 residues within 4Å: Chain V: C.66, A.326, V.349, P.350, C.383 Ligands: NI.65 2 PLIP interactions: 2 interactions with chain V Metal complexes: V:C.66, V:C.383 FE.73: 6 residues within 4Å: Chain Y: C.66, A.326, V.349, P.350, C.383 Ligands: NI.74 2 PLIP interactions: 2 interactions with chain Y Metal complexes: Y:C.66, Y:C.383 FE.82: 6 residues within 4Å: Chain 1: C.66, A.326, V.349, P.350, C.383 Ligands: NI.83 2 PLIP interactions: 2 interactions with chain 1 Metal complexes: 1:C.66, 1:C.383 FE.91: 6 residues within 4Å: Chain 4: C.66, A.326, V.349, P.350, C.383 Ligands: NI.92 2 PLIP interactions: 2 interactions with chain 4 Metal complexes: 4:C.66, 4:C.383 FE.100: 6 residues within 4Å: Chain 7: C.66, A.326, V.349, P.350, C.383 Ligands: NI.101 2 PLIP interactions: 2 interactions with chain 7 Metal complexes: 7:C.66, 7:C.383

12 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 5 residues within 4Å: Chain A: C.63, C.66, C.380, C.383 Ligands: FE.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.63, A:C.66, A:C.380, A:C.383 NI.11: 5 residues within 4Å: Chain D: C.63, C.66, C.380, C.383 Ligands: FE.10 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.63, D:C.66, D:C.380, D:C.383 NI.20: 5 residues within 4Å: Chain G: C.63, C.66, C.380, C.383 Ligands: FE.19 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.63, G:C.66, G:C.380, G:C.383 NI.29: 5 residues within 4Å: Chain J: C.63, C.66, C.380, C.383 Ligands: FE.28 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.63, J:C.66, J:C.380, J:C.383 NI.38: 5 residues within 4Å: Chain M: C.63, C.66, C.380, C.383 Ligands: FE.37 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.63, M:C.66, M:C.380, M:C.383 NI.47: 5 residues within 4Å: Chain P: C.63, C.66, C.380, C.383 Ligands: FE.46 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.63, P:C.66, P:C.380, P:C.383 NI.56: 5 residues within 4Å: Chain S: C.63, C.66, C.380, C.383 Ligands: FE.55 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.63, S:C.66, S:C.380, S:C.383 NI.65: 5 residues within 4Å: Chain V: C.63, C.66, C.380, C.383 Ligands: FE.64 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.63, V:C.66, V:C.380, V:C.383 NI.74: 5 residues within 4Å: Chain Y: C.63, C.66, C.380, C.383 Ligands: FE.73 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:C.63, Y:C.66, Y:C.380, Y:C.383 NI.83: 5 residues within 4Å: Chain 1: C.63, C.66, C.380, C.383 Ligands: FE.82 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:C.63, 1:C.66, 1:C.380, 1:C.383 NI.92: 5 residues within 4Å: Chain 4: C.63, C.66, C.380, C.383 Ligands: FE.91 4 PLIP interactions: 4 interactions with chain 4 Metal complexes: 4:C.63, 4:C.66, 4:C.380, 4:C.383 NI.101: 5 residues within 4Å: Chain 7: C.63, C.66, C.380, C.383 Ligands: FE.100 4 PLIP interactions: 4 interactions with chain 7 Metal complexes: 7:C.63, 7:C.66, 7:C.380, 7:C.383

12 x FE2: FE (II) ION(Non-covalent)

FE2.3: 3 residues within 4Å: Chain A: E.44, A.347, H.386 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.44, A:E.44, A:A.347, A:H.386 FE2.12: 3 residues within 4Å: Chain D: E.44, A.347, H.386 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.44, D:E.44, D:A.347, D:H.386 FE2.21: 3 residues within 4Å: Chain G: E.44, A.347, H.386 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.44, G:E.44, G:A.347, G:H.386 FE2.30: 3 residues within 4Å: Chain J: E.44, A.347, H.386 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.44, J:E.44, J:A.347, J:H.386 FE2.39: 3 residues within 4Å: Chain M: E.44, A.347, H.386 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:E.44, M:E.44, M:A.347, M:H.386 FE2.48: 3 residues within 4Å: Chain P: E.44, A.347, H.386 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:E.44, P:E.44, P:A.347, P:H.386 FE2.57: 3 residues within 4Å: Chain S: E.44, A.347, H.386 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:E.44, S:E.44, S:A.347, S:H.386 FE2.66: 3 residues within 4Å: Chain V: E.44, A.347, H.386 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:E.44, V:E.44, V:A.347, V:H.386 FE2.75: 3 residues within 4Å: Chain Y: E.44, A.347, H.386 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:E.44, Y:E.44, Y:A.347, Y:H.386 FE2.84: 3 residues within 4Å: Chain 1: E.44, A.347, H.386 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:E.44, 1:E.44, 1:A.347, 1:H.386 FE2.93: 3 residues within 4Å: Chain 4: E.44, A.347, H.386 4 PLIP interactions: 4 interactions with chain 4 Metal complexes: 4:E.44, 4:E.44, 4:A.347, 4:H.386 FE2.102: 3 residues within 4Å: Chain 7: E.44, A.347, H.386 4 PLIP interactions: 4 interactions with chain 7 Metal complexes: 7:E.44, 7:E.44, 7:A.347, 7:H.386

48 x SF4: IRON/SULFUR CLUSTER(Non-covalent)(Covalent)

SF4.4: 15 residues within 4Å: Chain A: R.61, H.150 Chain B: G.56, C.57, T.58, G.59, D.60, E.102, G.130, S.131, C.132, C.137, G.170, C.171, P.172 9 PLIP interactions: 9 interactions with chain B, Salt bridges: B:D.60, B:D.60, B:D.60, B:E.102 Metal complexes: B:C.57, B:D.60, B:D.60, B:C.132, B:C.171 SF4.5: 12 residues within 4Å: Chain B: A.229, C.230, T.232, A.234, L.235, C.249, I.250, K.251, C.252, G.253, I.254, C.255 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.230, B:C.249, B:C.252, B:C.255 SF4.6: 11 residues within 4Å: Chain B: C.220, I.221, G.222, C.223, G.224, T.225, C.226, M.237, P.242, C.259, P.260 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.220, B:C.223, B:C.226, B:C.259 SF4.8: 11 residues within 4Å: Chain B: I.221 Chain C: I.102, P.103, C.104, C.134, M.135, E.136, N.137, C.192, C.195, K.261 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.104, C:C.134, C:C.192, C:C.195 SF4.13: 15 residues within 4Å: Chain D: R.61, H.150 Chain E: G.56, C.57, T.58, G.59, D.60, E.102, G.130, S.131, C.132, C.137, G.170, C.171, P.172 9 PLIP interactions: 9 interactions with chain E, Salt bridges: E:D.60, E:D.60, E:D.60, E:E.102 Metal complexes: E:C.57, E:D.60, E:D.60, E:C.132, E:C.171 SF4.14: 12 residues within 4Å: Chain E: A.229, C.230, T.232, A.234, L.235, C.249, I.250, K.251, C.252, G.253, I.254, C.255 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.230, E:C.249, E:C.252, E:C.255 SF4.15: 11 residues within 4Å: Chain E: C.220, I.221, G.222, C.223, G.224, T.225, C.226, M.237, P.242, C.259, P.260 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.220, E:C.223, E:C.226, E:C.259 SF4.17: 11 residues within 4Å: Chain E: I.221 Chain F: I.102, P.103, C.104, C.134, M.135, E.136, N.137, C.192, C.195, K.261 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.104, F:C.134, F:C.192, F:C.195 SF4.22: 15 residues within 4Å: Chain G: R.61, H.150 Chain H: G.56, C.57, T.58, G.59, D.60, E.102, G.130, S.131, C.132, C.137, G.170, C.171, P.172 9 PLIP interactions: 9 interactions with chain H, Salt bridges: H:D.60, H:D.60, H:D.60, H:E.102 Metal complexes: H:C.57, H:D.60, H:D.60, H:C.132, H:C.171 SF4.23: 12 residues within 4Å: Chain H: A.229, C.230, T.232, A.234, L.235, C.249, I.250, K.251, C.252, G.253, I.254, C.255 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.230, H:C.249, H:C.252, H:C.255 SF4.24: 11 residues within 4Å: Chain H: C.220, I.221, G.222, C.223, G.224, T.225, C.226, M.237, P.242, C.259, P.260 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.220, H:C.223, H:C.226, H:C.259 SF4.26: 11 residues within 4Å: Chain H: I.221 Chain I: I.102, P.103, C.104, C.134, M.135, E.136, N.137, C.192, C.195, K.261 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.104, I:C.134, I:C.192, I:C.195 SF4.31: 15 residues within 4Å: Chain J: R.61, H.150 Chain K: G.56, C.57, T.58, G.59, D.60, E.102, G.130, S.131, C.132, C.137, G.170, C.171, P.172 9 PLIP interactions: 9 interactions with chain K, Salt bridges: K:D.60, K:D.60, K:D.60, K:E.102 Metal complexes: K:C.57, K:D.60, K:D.60, K:C.132, K:C.171 SF4.32: 12 residues within 4Å: Chain K: A.229, C.230, T.232, A.234, L.235, C.249, I.250, K.251, C.252, G.253, I.254, C.255 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.230, K:C.249, K:C.252, K:C.255 SF4.33: 11 residues within 4Å: Chain K: C.220, I.221, G.222, C.223, G.224, T.225, C.226, M.237, P.242, C.259, P.260 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.220, K:C.223, K:C.226, K:C.259 SF4.35: 11 residues within 4Å: Chain K: I.221 Chain L: I.102, P.103, C.104, C.134, M.135, E.136, N.137, C.192, C.195, K.261 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.104, L:C.134, L:C.192, L:C.195 SF4.40: 15 residues within 4Å: Chain M: R.61, H.150 Chain N: G.56, C.57, T.58, G.59, D.60, E.102, G.130, S.131, C.132, C.137, G.170, C.171, P.172 9 PLIP interactions: 9 interactions with chain N, Salt bridges: N:D.60, N:D.60, N:D.60, N:E.102 Metal complexes: N:C.57, N:D.60, N:D.60, N:C.132, N:C.171 SF4.41: 12 residues within 4Å: Chain N: A.229, C.230, T.232, A.234, L.235, C.249, I.250, K.251, C.252, G.253, I.254, C.255 4 PLIP interactions: 4 interactions with chain N, Metal complexes: N:C.230, N:C.249, N:C.252, N:C.255 SF4.42: 11 residues within 4Å: Chain N: C.220, I.221, G.222, C.223, G.224, T.225, C.226, M.237, P.242, C.259, P.260 4 PLIP interactions: 4 interactions with chain N, Metal complexes: N:C.220, N:C.223, N:C.226, N:C.259 SF4.44: 11 residues within 4Å: Chain N: I.221 Chain O: I.102, P.103, C.104, C.134, M.135, E.136, N.137, C.192, C.195, K.261 4 PLIP interactions: 4 interactions with chain O, Metal complexes: O:C.104, O:C.134, O:C.192, O:C.195 SF4.49: 15 residues within 4Å: Chain P: R.61, H.150 Chain Q: G.56, C.57, T.58, G.59, D.60, E.102, G.130, S.131, C.132, C.137, G.170, C.171, P.172 9 PLIP interactions: 9 interactions with chain Q, Salt bridges: Q:D.60, Q:D.60, Q:D.60, Q:E.102 Metal complexes: Q:C.57, Q:D.60, Q:D.60, Q:C.132, Q:C.171 SF4.50: 12 residues within 4Å: Chain Q: A.229, C.230, T.232, A.234, L.235, C.249, I.250, K.251, C.252, G.253, I.254, C.255 4 PLIP interactions: 4 interactions with chain Q, Metal complexes: Q:C.230, Q:C.249, Q:C.252, Q:C.255 SF4.51: 11 residues within 4Å: Chain Q: C.220, I.221, G.222, C.223, G.224, T.225, C.226, M.237, P.242, C.259, P.260 4 PLIP interactions: 4 interactions with chain Q, Metal complexes: Q:C.220, Q:C.223, Q:C.226, Q:C.259 SF4.53: 11 residues within 4Å: Chain Q: I.221 Chain R: I.102, P.103, C.104, C.134, M.135, E.136, N.137, C.192, C.195, K.261 4 PLIP interactions: 4 interactions with chain R, Metal complexes: R:C.104, R:C.134, R:C.192, R:C.195 SF4.58: 15 residues within 4Å: Chain S: R.61, H.150 Chain T: G.56, C.57, T.58, G.59, D.60, E.102, G.130, S.131, C.132, C.137, G.170, C.171, P.172 9 PLIP interactions: 9 interactions with chain T, Salt bridges: T:D.60, T:D.60, T:D.60, T:E.102 Metal complexes: T:C.57, T:D.60, T:D.60, T:C.132, T:C.171 SF4.59: 12 residues within 4Å: Chain T: A.229, C.230, T.232, A.234, L.235, C.249, I.250, K.251, C.252, G.253, I.254, C.255 4 PLIP interactions: 4 interactions with chain T, Metal complexes: T:C.230, T:C.249, T:C.252, T:C.255 SF4.60: 11 residues within 4Å: Chain T: C.220, I.221, G.222, C.223, G.224, T.225, C.226, M.237, P.242, C.259, P.260 4 PLIP interactions: 4 interactions with chain T, Metal complexes: T:C.220, T:C.223, T:C.226, T:C.259 SF4.62: 11 residues within 4Å: Chain T: I.221 Chain U: I.102, P.103, C.104, C.134, M.135, E.136, N.137, C.192, C.195, K.261 4 PLIP interactions: 4 interactions with chain U, Metal complexes: U:C.104, U:C.134, U:C.192, U:C.195 SF4.67: 15 residues within 4Å: Chain V: R.61, H.150 Chain W: G.56, C.57, T.58, G.59, D.60, E.102, G.130, S.131, C.132, C.137, G.170, C.171, P.172 9 PLIP interactions: 9 interactions with chain W, Salt bridges: W:D.60, W:D.60, W:D.60, W:E.102 Metal complexes: W:C.57, W:D.60, W:D.60, W:C.132, W:C.171 SF4.68: 12 residues within 4Å: Chain W: A.229, C.230, T.232, A.234, L.235, C.249, I.250, K.251, C.252, G.253, I.254, C.255 4 PLIP interactions: 4 interactions with chain W, Metal complexes: W:C.230, W:C.249, W:C.252, W:C.255 SF4.69: 11 residues within 4Å: Chain W: C.220, I.221, G.222, C.223, G.224, T.225, C.226, M.237, P.242, C.259, P.260 4 PLIP interactions: 4 interactions with chain W, Metal complexes: W:C.220, W:C.223, W:C.226, W:C.259 SF4.71: 11 residues within 4Å: Chain W: I.221 Chain X: I.102, P.103, C.104, C.134, M.135, E.136, N.137, C.192, C.195, K.261 4 PLIP interactions: 4 interactions with chain X, Metal complexes: X:C.104, X:C.134, X:C.192, X:C.195 SF4.76: 15 residues within 4Å: Chain Y: R.61, H.150 Chain Z: G.56, C.57, T.58, G.59, D.60, E.102, G.130, S.131, C.132, C.137, G.170, C.171, P.172 9 PLIP interactions: 9 interactions with chain Z, Salt bridges: Z:D.60, Z:D.60, Z:D.60, Z:E.102 Metal complexes: Z:C.57, Z:D.60, Z:D.60, Z:C.132, Z:C.171 SF4.77: 12 residues within 4Å: Chain Z: A.229, C.230, T.232, A.234, L.235, C.249, I.250, K.251, C.252, G.253, I.254, C.255 4 PLIP interactions: 4 interactions with chain Z, Metal complexes: Z:C.230, Z:C.249, Z:C.252, Z:C.255 SF4.78: 11 residues within 4Å: Chain Z: C.220, I.221, G.222, C.223, G.224, T.225, C.226, M.237, P.242, C.259, P.260 4 PLIP interactions: 4 interactions with chain Z, Metal complexes: Z:C.220, Z:C.223, Z:C.226, Z:C.259 SF4.80: 11 residues within 4Å: Chain 0: I.102, P.103, C.104, C.134, M.135, E.136, N.137, C.192, C.195, K.261 Chain Z: I.221 4 PLIP interactions: 4 interactions with chain 0, Metal complexes: 0:C.104, 0:C.134, 0:C.192, 0:C.195 SF4.85: 15 residues within 4Å: Chain 1: R.61, H.150 Chain 2: G.56, C.57, T.58, G.59, D.60, E.102, G.130, S.131, C.132, C.137, G.170, C.171, P.172 9 PLIP interactions: 9 interactions with chain 2, Salt bridges: 2:D.60, 2:D.60, 2:D.60, 2:E.102 Metal complexes: 2:C.57, 2:D.60, 2:D.60, 2:C.132, 2:C.171 SF4.86: 12 residues within 4Å: Chain 2: A.229, C.230, T.232, A.234, L.235, C.249, I.250, K.251, C.252, G.253, I.254, C.255 4 PLIP interactions: 4 interactions with chain 2, Metal complexes: 2:C.230, 2:C.249, 2:C.252, 2:C.255 SF4.87: 11 residues within 4Å: Chain 2: C.220, I.221, G.222, C.223, G.224, T.225, C.226, M.237, P.242, C.259, P.260 4 PLIP interactions: 4 interactions with chain 2, Metal complexes: 2:C.220, 2:C.223, 2:C.226, 2:C.259 SF4.89: 11 residues within 4Å: Chain 2: I.221 Chain 3: I.102, P.103, C.104, C.134, M.135, E.136, N.137, C.192, C.195, K.261 4 PLIP interactions: 4 interactions with chain 3, Metal complexes: 3:C.104, 3:C.134, 3:C.192, 3:C.195 SF4.94: 15 residues within 4Å: Chain 4: R.61, H.150 Chain 5: G.56, C.57, T.58, G.59, D.60, E.102, G.130, S.131, C.132, C.137, G.170, C.171, P.172 9 PLIP interactions: 9 interactions with chain 5, Salt bridges: 5:D.60, 5:D.60, 5:D.60, 5:E.102 Metal complexes: 5:C.57, 5:D.60, 5:D.60, 5:C.132, 5:C.171 SF4.95: 12 residues within 4Å: Chain 5: A.229, C.230, T.232, A.234, L.235, C.249, I.250, K.251, C.252, G.253, I.254, C.255 4 PLIP interactions: 4 interactions with chain 5, Metal complexes: 5:C.230, 5:C.249, 5:C.252, 5:C.255 SF4.96: 11 residues within 4Å: Chain 5: C.220, I.221, G.222, C.223, G.224, T.225, C.226, M.237, P.242, C.259, P.260 4 PLIP interactions: 4 interactions with chain 5, Metal complexes: 5:C.220, 5:C.223, 5:C.226, 5:C.259 SF4.98: 11 residues within 4Å: Chain 5: I.221 Chain 6: I.102, P.103, C.104, C.134, M.135, E.136, N.137, C.192, C.195, K.261 4 PLIP interactions: 4 interactions with chain 6, Metal complexes: 6:C.104, 6:C.134, 6:C.192, 6:C.195 SF4.103: 15 residues within 4Å: Chain 7: R.61, H.150 Chain 8: G.56, C.57, T.58, G.59, D.60, E.102, G.130, S.131, C.132, C.137, G.170, C.171, P.172 9 PLIP interactions: 9 interactions with chain 8, Salt bridges: 8:D.60, 8:D.60, 8:D.60, 8:E.102 Metal complexes: 8:C.57, 8:D.60, 8:D.60, 8:C.132, 8:C.171 SF4.104: 12 residues within 4Å: Chain 8: A.229, C.230, T.232, A.234, L.235, C.249, I.250, K.251, C.252, G.253, I.254, C.255 4 PLIP interactions: 4 interactions with chain 8, Metal complexes: 8:C.230, 8:C.249, 8:C.252, 8:C.255 SF4.105: 11 residues within 4Å: Chain 8: C.220, I.221, G.222, C.223, G.224, T.225, C.226, M.237, P.242, C.259, P.260 4 PLIP interactions: 4 interactions with chain 8, Metal complexes: 8:C.220, 8:C.223, 8:C.226, 8:C.259 SF4.107: 11 residues within 4Å: Chain 8: I.221 Chain 9: I.102, P.103, C.104, C.134, M.135, E.136, N.137, C.192, C.195, K.261 4 PLIP interactions: 4 interactions with chain 9, Metal complexes: 9:C.104, 9:C.134, 9:C.192, 9:C.195

12 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain B: C.206, C.208 Chain K: C.206, C.208 Ligands: ZN.34 4 PLIP interactions: 2 interactions with chain K, 2 interactions with chain B Metal complexes: K:C.206, K:C.208, B:C.206, B:C.208 ZN.16: 5 residues within 4Å: Chain E: C.206, C.208 Chain H: C.206, C.208 Ligands: ZN.25 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain H Metal complexes: E:C.206, E:C.208, H:C.206, H:C.208 ZN.25: 5 residues within 4Å: Chain E: C.206, C.208 Chain H: C.206, C.208 Ligands: ZN.16 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain H Metal complexes: E:C.206, E:C.208, H:C.206, H:C.208 ZN.34: 5 residues within 4Å: Chain B: C.206, C.208 Chain K: C.206, C.208 Ligands: ZN.7 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain K Metal complexes: B:C.206, B:C.208, K:C.206, K:C.208 ZN.43: 5 residues within 4Å: Chain N: C.206, C.208 Chain W: C.206, C.208 Ligands: ZN.70 4 PLIP interactions: 2 interactions with chain W, 2 interactions with chain N Metal complexes: W:C.206, W:C.208, N:C.206, N:C.208 ZN.52: 5 residues within 4Å: Chain Q: C.206, C.208 Chain T: C.206, C.208 Ligands: ZN.61 4 PLIP interactions: 2 interactions with chain Q, 2 interactions with chain T Metal complexes: Q:C.206, Q:C.208, T:C.206, T:C.208 ZN.61: 5 residues within 4Å: Chain Q: C.206, C.208 Chain T: C.206, C.208 Ligands: ZN.52 4 PLIP interactions: 2 interactions with chain Q, 2 interactions with chain T Metal complexes: Q:C.206, Q:C.208, T:C.206, T:C.208 ZN.70: 5 residues within 4Å: Chain N: C.206, C.208 Chain W: C.206, C.208 Ligands: ZN.43 4 PLIP interactions: 2 interactions with chain N, 2 interactions with chain W Metal complexes: N:C.206, N:C.208, W:C.206, W:C.208 ZN.79: 5 residues within 4Å: Chain 8: C.206, C.208 Chain Z: C.206, C.208 Ligands: ZN.106 4 PLIP interactions: 2 interactions with chain 8, 2 interactions with chain Z Metal complexes: 8:C.206, 8:C.208, Z:C.206, Z:C.208 ZN.88: 5 residues within 4Å: Chain 2: C.206, C.208 Chain 5: C.206, C.208 Ligands: ZN.97 4 PLIP interactions: 2 interactions with chain 2, 2 interactions with chain 5 Metal complexes: 2:C.206, 2:C.208, 5:C.206, 5:C.208 ZN.97: 5 residues within 4Å: Chain 2: C.206, C.208 Chain 5: C.206, C.208 Ligands: ZN.88 4 PLIP interactions: 2 interactions with chain 5, 2 interactions with chain 2 Metal complexes: 5:C.206, 5:C.208, 2:C.206, 2:C.208 ZN.106: 5 residues within 4Å: Chain 8: C.206, C.208 Chain Z: C.206, C.208 Ligands: ZN.79 4 PLIP interactions: 2 interactions with chain 8, 2 interactions with chain Z Metal complexes: 8:C.206, 8:C.208, Z:C.206, Z:C.208

12 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.9: 32 residues within 4Å: Chain C: A.23, Q.24, D.25, G.26, G.27, I.28, V.29, T.30, V.47, A.48, A.71, A.72, G.73, T.74, K.75, Y.76, T.77, S.79, N.81, V.100, I.102, Q.105, I.132, Y.133, C.134, M.135, N.137, Y.198, T.207, G.208, S.209, V.210 30 PLIP interactions: 30 interactions with chain C Hydrophobic interactions: C:T.74, C:Y.76, C:Y.76, C:I.102, C:I.132, C:N.137 Hydrogen bonds: C:Q.24, C:D.25, C:G.26, C:G.27, C:I.28, C:V.29, C:T.30, C:T.30, C:A.48, C:A.48, C:G.73, C:T.74, C:T.74, C:K.75, C:K.75, C:Y.76, C:T.77, C:S.79, C:N.81, C:M.135, C:Y.198, C:Y.198, C:S.209, C:V.210 FAD.18: 32 residues within 4Å: Chain F: A.23, Q.24, D.25, G.26, G.27, I.28, V.29, T.30, V.47, A.48, A.71, A.72, G.73, T.74, K.75, Y.76, T.77, S.79, N.81, V.100, I.102, Q.105, I.132, Y.133, C.134, M.135, N.137, Y.198, T.207, G.208, S.209, V.210 27 PLIP interactions: 27 interactions with chain F Hydrophobic interactions: F:T.74, F:Y.76, F:I.102, F:I.132, F:N.137 Hydrogen bonds: F:Q.24, F:D.25, F:G.26, F:G.27, F:I.28, F:V.29, F:T.30, F:A.48, F:A.48, F:G.73, F:T.74, F:K.75, F:K.75, F:Y.76, F:T.77, F:S.79, F:N.81, F:M.135, F:Y.198, F:Y.198, F:S.209, F:V.210 FAD.27: 32 residues within 4Å: Chain I: A.23, Q.24, D.25, G.26, G.27, I.28, V.29, T.30, V.47, A.48, A.71, A.72, G.73, T.74, K.75, Y.76, T.77, S.79, N.81, V.100, I.102, Q.105, I.132, Y.133, C.134, M.135, N.137, Y.198, T.207, G.208, S.209, V.210 28 PLIP interactions: 28 interactions with chain I Hydrophobic interactions: I:T.74, I:Y.76, I:Y.76, I:I.102, I:I.132, I:N.137 Hydrogen bonds: I:Q.24, I:D.25, I:G.26, I:G.27, I:I.28, I:V.29, I:T.30, I:A.48, I:A.48, I:G.73, I:T.74, I:K.75, I:K.75, I:Y.76, I:T.77, I:S.79, I:N.81, I:M.135, I:Y.198, I:Y.198, I:S.209, I:V.210 FAD.36: 32 residues within 4Å: Chain L: A.23, Q.24, D.25, G.26, G.27, I.28, V.29, T.30, V.47, A.48, A.71, A.72, G.73, T.74, K.75, Y.76, T.77, S.79, N.81, V.100, I.102, Q.105, I.132, Y.133, C.134, M.135, N.137, Y.198, T.207, G.208, S.209, V.210 30 PLIP interactions: 30 interactions with chain L Hydrophobic interactions: L:T.74, L:Y.76, L:Y.76, L:I.102, L:I.132, L:N.137 Hydrogen bonds: L:Q.24, L:D.25, L:G.26, L:G.27, L:I.28, L:V.29, L:T.30, L:T.30, L:A.48, L:A.48, L:G.73, L:T.74, L:T.74, L:K.75, L:K.75, L:Y.76, L:T.77, L:S.79, L:N.81, L:M.135, L:Y.198, L:Y.198, L:S.209, L:V.210 FAD.45: 32 residues within 4Å: Chain O: A.23, Q.24, D.25, G.26, G.27, I.28, V.29, T.30, V.47, A.48, A.71, A.72, G.73, T.74, K.75, Y.76, T.77, S.79, N.81, V.100, I.102, Q.105, I.132, Y.133, C.134, M.135, N.137, Y.198, T.207, G.208, S.209, V.210 29 PLIP interactions: 29 interactions with chain O Hydrophobic interactions: O:T.74, O:Y.76, O:I.102, O:I.132, O:N.137 Hydrogen bonds: O:Q.24, O:D.25, O:G.26, O:G.27, O:I.28, O:V.29, O:T.30, O:T.30, O:A.48, O:A.48, O:G.73, O:T.74, O:T.74, O:K.75, O:K.75, O:Y.76, O:T.77, O:S.79, O:N.81, O:M.135, O:Y.198, O:Y.198, O:S.209, O:V.210 FAD.54: 32 residues within 4Å: Chain R: A.23, Q.24, D.25, G.26, G.27, I.28, V.29, T.30, V.47, A.48, A.71, A.72, G.73, T.74, K.75, Y.76, T.77, S.79, N.81, V.100, I.102, Q.105, I.132, Y.133, C.134, M.135, N.137, Y.198, T.207, G.208, S.209, V.210 28 PLIP interactions: 28 interactions with chain R Hydrophobic interactions: R:T.74, R:Y.76, R:Y.76, R:I.102, R:I.132, R:N.137 Hydrogen bonds: R:Q.24, R:D.25, R:G.26, R:G.27, R:I.28, R:V.29, R:T.30, R:A.48, R:A.48, R:G.73, R:T.74, R:K.75, R:K.75, R:Y.76, R:T.77, R:S.79, R:N.81, R:M.135, R:Y.198, R:Y.198, R:S.209, R:V.210 FAD.63: 32 residues within 4Å: Chain U: A.23, Q.24, D.25, G.26, G.27, I.28, V.29, T.30, V.47, A.48, A.71, A.72, G.73, T.74, K.75, Y.76, T.77, S.79, N.81, V.100, I.102, Q.105, I.132, Y.133, C.134, M.135, N.137, Y.198, T.207, G.208, S.209, V.210 27 PLIP interactions: 27 interactions with chain U Hydrophobic interactions: U:T.74, U:Y.76, U:I.102, U:I.132, U:N.137 Hydrogen bonds: U:Q.24, U:D.25, U:G.26, U:G.27, U:I.28, U:V.29, U:T.30, U:A.48, U:A.48, U:G.73, U:T.74, U:K.75, U:K.75, U:Y.76, U:T.77, U:S.79, U:N.81, U:M.135, U:Y.198, U:Y.198, U:S.209, U:V.210 FAD.72: 32 residues within 4Å: Chain X: A.23, Q.24, D.25, G.26, G.27, I.28, V.29, T.30, V.47, A.48, A.71, A.72, G.73, T.74, K.75, Y.76, T.77, S.79, N.81, V.100, I.102, Q.105, I.132, Y.133, C.134, M.135, N.137, Y.198, T.207, G.208, S.209, V.210 30 PLIP interactions: 30 interactions with chain X Hydrophobic interactions: X:T.74, X:Y.76, X:Y.76, X:I.102, X:I.132, X:N.137 Hydrogen bonds: X:Q.24, X:D.25, X:G.26, X:G.27, X:I.28, X:V.29, X:T.30, X:T.30, X:A.48, X:A.48, X:G.73, X:T.74, X:T.74, X:K.75, X:K.75, X:Y.76, X:T.77, X:S.79, X:N.81, X:M.135, X:Y.198, X:Y.198, X:S.209, X:V.210 FAD.81: 32 residues within 4Å: Chain 0: A.23, Q.24, D.25, G.26, G.27, I.28, V.29, T.30, V.47, A.48, A.71, A.72, G.73, T.74, K.75, Y.76, T.77, S.79, N.81, V.100, I.102, Q.105, I.132, Y.133, C.134, M.135, N.137, Y.198, T.207, G.208, S.209, V.210 29 PLIP interactions: 29 interactions with chain 0 Hydrophobic interactions: 0:T.74, 0:Y.76, 0:I.102, 0:I.132, 0:N.137 Hydrogen bonds: 0:Q.24, 0:D.25, 0:G.26, 0:G.27, 0:I.28, 0:V.29, 0:T.30, 0:T.30, 0:A.48, 0:A.48, 0:G.73, 0:T.74, 0:T.74, 0:K.75, 0:K.75, 0:Y.76, 0:T.77, 0:S.79, 0:N.81, 0:M.135, 0:Y.198, 0:Y.198, 0:S.209, 0:V.210 FAD.90: 32 residues within 4Å: Chain 3: A.23, Q.24, D.25, G.26, G.27, I.28, V.29, T.30, V.47, A.48, A.71, A.72, G.73, T.74, K.75, Y.76, T.77, S.79, N.81, V.100, I.102, Q.105, I.132, Y.133, C.134, M.135, N.137, Y.198, T.207, G.208, S.209, V.210 28 PLIP interactions: 28 interactions with chain 3 Hydrophobic interactions: 3:T.74, 3:Y.76, 3:Y.76, 3:I.102, 3:I.132, 3:N.137 Hydrogen bonds: 3:Q.24, 3:D.25, 3:G.26, 3:G.27, 3:I.28, 3:V.29, 3:T.30, 3:A.48, 3:A.48, 3:G.73, 3:T.74, 3:K.75, 3:K.75, 3:Y.76, 3:T.77, 3:S.79, 3:N.81, 3:M.135, 3:Y.198, 3:Y.198, 3:S.209, 3:V.210 FAD.99: 32 residues within 4Å: Chain 6: A.23, Q.24, D.25, G.26, G.27, I.28, V.29, T.30, V.47, A.48, A.71, A.72, G.73, T.74, K.75, Y.76, T.77, S.79, N.81, V.100, I.102, Q.105, I.132, Y.133, C.134, M.135, N.137, Y.198, T.207, G.208, S.209, V.210 28 PLIP interactions: 28 interactions with chain 6 Hydrophobic interactions: 6:T.74, 6:Y.76, 6:Y.76, 6:I.102, 6:I.132, 6:N.137 Hydrogen bonds: 6:Q.24, 6:D.25, 6:G.26, 6:G.27, 6:I.28, 6:V.29, 6:T.30, 6:A.48, 6:A.48, 6:G.73, 6:T.74, 6:K.75, 6:K.75, 6:Y.76, 6:T.77, 6:S.79, 6:N.81, 6:M.135, 6:Y.198, 6:Y.198, 6:S.209, 6:V.210 FAD.108: 32 residues within 4Å: Chain 9: A.23, Q.24, D.25, G.26, G.27, I.28, V.29, T.30, V.47, A.48, A.71, A.72, G.73, T.74, K.75, Y.76, T.77, S.79, N.81, V.100, I.102, Q.105, I.132, Y.133, C.134, M.135, N.137, Y.198, T.207, G.208, S.209, V.210 29 PLIP interactions: 29 interactions with chain 9 Hydrophobic interactions: 9:T.74, 9:Y.76, 9:I.102, 9:I.132, 9:N.137 Hydrogen bonds: 9:Q.24, 9:D.25, 9:G.26, 9:G.27, 9:I.28, 9:V.29, 9:T.30, 9:T.30, 9:A.48, 9:A.48, 9:G.73, 9:T.74, 9:T.74, 9:K.75, 9:K.75, 9:Y.76, 9:T.77, 9:S.79, 9:N.81, 9:M.135, 9:Y.198, 9:Y.198, 9:S.209, 9:V.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Allegretti, M. et al., Atomic Model of the F420-Reducing [Nife] Hydrogenase by Electron Cryo-Electron Microscopy Using a Direct Electron Detector. Elife (2014)

Release Date

2014-02-26

Peptides

F420-REDUCING HYDROGENASE, SUBUNIT ALPHA: ADGJMPSVY147
F420-REDUCING HYDROGENASE, SUBUNIT GAMMA: BEHKNQTWZ258
F420-REDUCING HYDROGENASE, SUBUNIT BETA: CFILORUX0369

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

M
A

P
A

S
A

V
A

Y
A

1
A

4
A

7
A

B
B

E
B

H
B

K
B

N
B

Q
B

T
B

W
B

Z
B

2
B

5
B

8
B

C
C

F
C

I
C

L
C

O
C

R
C

U
C

X
C

0
C

3
C

6
C

9
C

F420-REDUCING HYDROGENASE, SUBUNIT ALPHA

F420-REDUCING HYDROGENASE, SUBUNIT GAMMA

F420-REDUCING HYDROGENASE, SUBUNIT BETA

Related Entries With Identical Sequence