SMTL ID : 1nfv.2 (2 other biounits)

X-ray structure of Desulfovibrio desulfuricans bacterioferritin: the diiron centre in different catalytic states (as-isolated structure)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: E.23, E.56, H.59, E.132 Ligands: FE.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.23, A:E.23, A:E.56, A:H.59, A:E.132 FE.2: 5 residues within 4Å: Chain A: E.56, E.99, E.132, H.135 Ligands: FE.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.56, A:E.99, A:E.99, A:E.132, A:H.135 FE.7: 5 residues within 4Å: Chain B: E.23, E.56, H.59, E.132 Ligands: FE.8 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.23, B:E.23, B:E.56, B:H.59, B:E.132 FE.8: 5 residues within 4Å: Chain B: E.56, E.99, E.132, H.135 Ligands: FE.7 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.56, B:E.99, B:E.99, B:E.132, B:H.135 FE.15: 5 residues within 4Å: Chain C: E.23, E.56, H.59, E.132 Ligands: FE.16 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.23, C:E.23, C:E.56, C:H.59, C:E.132 FE.16: 5 residues within 4Å: Chain C: E.56, E.99, E.132, H.135 Ligands: FE.15 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.56, C:E.99, C:E.99, C:E.132, C:H.135 FE.21: 5 residues within 4Å: Chain D: E.23, E.56, H.59, E.132 Ligands: FE.22 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.23, D:E.23, D:E.56, D:H.59, D:E.132 FE.22: 5 residues within 4Å: Chain D: E.56, E.99, E.132, H.135 Ligands: FE.21 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.56, D:E.99, D:E.99, D:E.132, D:H.135 FE.30: 5 residues within 4Å: Chain E: E.23, E.56, H.59, E.132 Ligands: FE.31 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.23, E:E.23, E:E.56, E:H.59, E:E.132 FE.31: 5 residues within 4Å: Chain E: E.56, E.99, E.132, H.135 Ligands: FE.30 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.56, E:E.99, E:E.99, E:E.132, E:H.135 FE.36: 5 residues within 4Å: Chain F: E.23, E.56, H.59, E.132 Ligands: FE.37 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.23, F:E.23, F:E.56, F:H.59, F:E.132 FE.37: 5 residues within 4Å: Chain F: E.56, E.99, E.132, H.135 Ligands: FE.36 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.56, F:E.99, F:E.99, F:E.132, F:H.135 FE.43: 5 residues within 4Å: Chain G: E.23, E.56, H.59, E.132 Ligands: FE.44 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.23, G:E.23, G:E.56, G:H.59, G:E.132 FE.44: 5 residues within 4Å: Chain G: E.56, E.99, E.132, H.135 Ligands: FE.43 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.56, G:E.99, G:E.99, G:E.132, G:H.135 FE.49: 5 residues within 4Å: Chain H: E.23, E.56, H.59, E.132 Ligands: FE.50 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.23, H:E.23, H:E.56, H:H.59, H:E.132 FE.50: 5 residues within 4Å: Chain H: E.56, E.99, E.132, H.135 Ligands: FE.49 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.56, H:E.99, H:E.99, H:E.132, H:H.135 FE.56: 5 residues within 4Å: Chain I: E.23, E.56, H.59, E.132 Ligands: FE.57 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:E.23, I:E.23, I:E.56, I:H.59, I:E.132 FE.57: 5 residues within 4Å: Chain I: E.56, E.99, E.132, H.135 Ligands: FE.56 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:E.56, I:E.99, I:E.99, I:E.132, I:H.135 FE.62: 5 residues within 4Å: Chain J: E.23, E.56, H.59, E.132 Ligands: FE.63 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:E.23, J:E.23, J:E.56, J:H.59, J:E.132 FE.63: 5 residues within 4Å: Chain J: E.56, E.99, E.132, H.135 Ligands: FE.62 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:E.56, J:E.99, J:E.99, J:E.132, J:H.135 FE.70: 5 residues within 4Å: Chain K: E.23, E.56, H.59, E.132 Ligands: FE.71 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:E.23, K:E.23, K:E.56, K:H.59, K:E.132 FE.71: 5 residues within 4Å: Chain K: E.56, E.99, E.132, H.135 Ligands: FE.70 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:E.56, K:E.99, K:E.99, K:E.132, K:H.135 FE.76: 5 residues within 4Å: Chain L: E.23, E.56, H.59, E.132 Ligands: FE.77 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:E.23, L:E.23, L:E.56, L:H.59, L:E.132 FE.77: 5 residues within 4Å: Chain L: E.56, E.99, E.132, H.135 Ligands: FE.76 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:E.56, L:E.99, L:E.99, L:E.132, L:H.135 FE.85: 5 residues within 4Å: Chain M: E.23, E.56, H.59, E.132 Ligands: FE.86 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:E.23, M:E.23, M:E.56, M:H.59, M:E.132 FE.86: 5 residues within 4Å: Chain M: E.56, E.99, E.132, H.135 Ligands: FE.85 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:E.56, M:E.99, M:E.99, M:E.132, M:H.135 FE.91: 5 residues within 4Å: Chain N: E.23, E.56, H.59, E.132 Ligands: FE.92 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:E.23, N:E.23, N:E.56, N:H.59, N:E.132 FE.92: 5 residues within 4Å: Chain N: E.56, E.99, E.132, H.135 Ligands: FE.91 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:E.56, N:E.99, N:E.99, N:E.132, N:H.135 FE.98: 5 residues within 4Å: Chain O: E.23, E.56, H.59, E.132 Ligands: FE.99 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:E.23, O:E.23, O:E.56, O:H.59, O:E.132 FE.99: 5 residues within 4Å: Chain O: E.56, E.99, E.132, H.135 Ligands: FE.98 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:E.56, O:E.99, O:E.99, O:E.132, O:H.135 FE.104: 5 residues within 4Å: Chain P: E.23, E.56, H.59, E.132 Ligands: FE.105 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:E.23, P:E.23, P:E.56, P:H.59, P:E.132 FE.105: 5 residues within 4Å: Chain P: E.56, E.99, E.132, H.135 Ligands: FE.104 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:E.56, P:E.99, P:E.99, P:E.132, P:H.135 FE.111: 5 residues within 4Å: Chain Q: E.23, E.56, H.59, E.132 Ligands: FE.112 5 PLIP interactions: 5 interactions with chain Q Metal complexes: Q:E.23, Q:E.23, Q:E.56, Q:H.59, Q:E.132 FE.112: 5 residues within 4Å: Chain Q: E.56, E.99, E.132, H.135 Ligands: FE.111 5 PLIP interactions: 5 interactions with chain Q Metal complexes: Q:E.56, Q:E.99, Q:E.99, Q:E.132, Q:H.135 FE.117: 5 residues within 4Å: Chain R: E.23, E.56, H.59, E.132 Ligands: FE.118 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:E.23, R:E.23, R:E.56, R:H.59, R:E.132 FE.118: 5 residues within 4Å: Chain R: E.56, E.99, E.132, H.135 Ligands: FE.117 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:E.56, R:E.99, R:E.99, R:E.132, R:H.135 FE.125: 5 residues within 4Å: Chain S: E.23, E.56, H.59, E.132 Ligands: FE.126 5 PLIP interactions: 5 interactions with chain S Metal complexes: S:E.23, S:E.23, S:E.56, S:H.59, S:E.132 FE.126: 5 residues within 4Å: Chain S: E.56, E.99, E.132, H.135 Ligands: FE.125 5 PLIP interactions: 5 interactions with chain S Metal complexes: S:E.56, S:E.99, S:E.99, S:E.132, S:H.135 FE.131: 5 residues within 4Å: Chain T: E.23, E.56, H.59, E.132 Ligands: FE.132 5 PLIP interactions: 5 interactions with chain T Metal complexes: T:E.23, T:E.23, T:E.56, T:H.59, T:E.132 FE.132: 5 residues within 4Å: Chain T: E.56, E.99, E.132, H.135 Ligands: FE.131 5 PLIP interactions: 5 interactions with chain T Metal complexes: T:E.56, T:E.99, T:E.99, T:E.132, T:H.135 FE.140: 5 residues within 4Å: Chain U: E.23, E.56, H.59, E.132 Ligands: FE.141 5 PLIP interactions: 5 interactions with chain U Metal complexes: U:E.23, U:E.23, U:E.56, U:H.59, U:E.132 FE.141: 5 residues within 4Å: Chain U: E.56, E.99, E.132, H.135 Ligands: FE.140 5 PLIP interactions: 5 interactions with chain U Metal complexes: U:E.56, U:E.99, U:E.99, U:E.132, U:H.135 FE.146: 5 residues within 4Å: Chain V: E.23, E.56, H.59, E.132 Ligands: FE.147 5 PLIP interactions: 5 interactions with chain V Metal complexes: V:E.23, V:E.23, V:E.56, V:H.59, V:E.132 FE.147: 5 residues within 4Å: Chain V: E.56, E.99, E.132, H.135 Ligands: FE.146 5 PLIP interactions: 5 interactions with chain V Metal complexes: V:E.56, V:E.99, V:E.99, V:E.132, V:H.135 FE.153: 5 residues within 4Å: Chain W: E.23, E.56, H.59, E.132 Ligands: FE.154 5 PLIP interactions: 5 interactions with chain W Metal complexes: W:E.23, W:E.23, W:E.56, W:H.59, W:E.132 FE.154: 5 residues within 4Å: Chain W: E.56, E.99, E.132, H.135 Ligands: FE.153 5 PLIP interactions: 5 interactions with chain W Metal complexes: W:E.56, W:E.99, W:E.99, W:E.132, W:H.135 FE.159: 5 residues within 4Å: Chain X: E.23, E.56, H.59, E.132 Ligands: FE.160 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:E.23, X:E.23, X:E.56, X:H.59, X:E.132 FE.160: 5 residues within 4Å: Chain X: E.56, E.99, E.132, H.135 Ligands: FE.159 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:E.56, X:E.99, X:E.99, X:E.132, X:H.135

72 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: S.144, K.147, N.148 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: P.161, S.162, S.163 Ligand excluded by PLIP SO4.9: 6 residues within 4Å: Chain B: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.12 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain B: S.144, K.147, N.148 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain B: K.114 Chain C: K.114 Chain W: K.114 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain C: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain C: P.161, S.162, S.163 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain D: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain D: N.4, R.5 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain D: P.161, S.162, S.163 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain D: K.114 Chain E: K.114 Chain H: K.114 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain E: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain E: S.144, K.147, N.148 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain E: P.161, S.162, S.163 Ligand excluded by PLIP SO4.38: 6 residues within 4Å: Chain F: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.42 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain F: N.4, R.5 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain F: S.144, K.147, N.148 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain F: G.150, D.151, T.152 Chain U: T.152 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain G: P.161, S.162, S.163 Ligand excluded by PLIP SO4.46: 4 residues within 4Å: Chain G: R.123, R.127 Chain K: R.123, R.127 Ligand excluded by PLIP SO4.51: 6 residues within 4Å: Chain H: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.54 Ligand excluded by PLIP SO4.52: 2 residues within 4Å: Chain H: S.144, N.148 Ligand excluded by PLIP SO4.53: 3 residues within 4Å: Chain H: P.161, S.162, S.163 Ligand excluded by PLIP SO4.58: 5 residues within 4Å: Chain I: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.59: 3 residues within 4Å: Chain I: S.144, K.147, N.148 Ligand excluded by PLIP SO4.60: 3 residues within 4Å: Chain I: P.161, S.162, S.163 Ligand excluded by PLIP SO4.64: 6 residues within 4Å: Chain J: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.67 Ligand excluded by PLIP SO4.65: 3 residues within 4Å: Chain J: S.144, K.147, N.148 Ligand excluded by PLIP SO4.69: 3 residues within 4Å: Chain G: K.114 Chain J: K.114 Chain K: K.114 Ligand excluded by PLIP SO4.72: 5 residues within 4Å: Chain K: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.73: 3 residues within 4Å: Chain K: P.161, S.162, S.163 Ligand excluded by PLIP SO4.78: 5 residues within 4Å: Chain L: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.79: 2 residues within 4Å: Chain L: N.4, R.5 Ligand excluded by PLIP SO4.80: 3 residues within 4Å: Chain L: P.161, S.162, S.163 Ligand excluded by PLIP SO4.84: 3 residues within 4Å: Chain L: K.114 Chain M: K.114 Chain P: K.114 Ligand excluded by PLIP SO4.87: 5 residues within 4Å: Chain M: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.88: 3 residues within 4Å: Chain M: S.144, K.147, N.148 Ligand excluded by PLIP SO4.89: 3 residues within 4Å: Chain M: P.161, S.162, S.163 Ligand excluded by PLIP SO4.93: 6 residues within 4Å: Chain N: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.97 Ligand excluded by PLIP SO4.94: 2 residues within 4Å: Chain N: N.4, R.5 Ligand excluded by PLIP SO4.95: 3 residues within 4Å: Chain N: S.144, K.147, N.148 Ligand excluded by PLIP SO4.96: 4 residues within 4Å: Chain E: T.152 Chain N: G.150, D.151, T.152 Ligand excluded by PLIP SO4.100: 3 residues within 4Å: Chain O: P.161, S.162, S.163 Ligand excluded by PLIP SO4.101: 4 residues within 4Å: Chain O: R.123, R.127 Chain S: R.123, R.127 Ligand excluded by PLIP SO4.106: 6 residues within 4Å: Chain P: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.109 Ligand excluded by PLIP SO4.107: 2 residues within 4Å: Chain P: S.144, N.148 Ligand excluded by PLIP SO4.108: 3 residues within 4Å: Chain P: P.161, S.162, S.163 Ligand excluded by PLIP SO4.113: 5 residues within 4Å: Chain Q: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.114: 3 residues within 4Å: Chain Q: S.144, K.147, N.148 Ligand excluded by PLIP SO4.115: 3 residues within 4Å: Chain Q: P.161, S.162, S.163 Ligand excluded by PLIP SO4.119: 6 residues within 4Å: Chain R: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.122 Ligand excluded by PLIP SO4.120: 3 residues within 4Å: Chain R: S.144, K.147, N.148 Ligand excluded by PLIP SO4.124: 3 residues within 4Å: Chain O: K.114 Chain R: K.114 Chain S: K.114 Ligand excluded by PLIP SO4.127: 5 residues within 4Å: Chain S: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.128: 3 residues within 4Å: Chain S: P.161, S.162, S.163 Ligand excluded by PLIP SO4.133: 5 residues within 4Å: Chain T: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.134: 2 residues within 4Å: Chain T: N.4, R.5 Ligand excluded by PLIP SO4.135: 3 residues within 4Å: Chain T: P.161, S.162, S.163 Ligand excluded by PLIP SO4.139: 3 residues within 4Å: Chain T: K.114 Chain U: K.114 Chain X: K.114 Ligand excluded by PLIP SO4.142: 5 residues within 4Å: Chain U: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.143: 3 residues within 4Å: Chain U: S.144, K.147, N.148 Ligand excluded by PLIP SO4.144: 3 residues within 4Å: Chain U: P.161, S.162, S.163 Ligand excluded by PLIP SO4.148: 6 residues within 4Å: Chain V: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.152 Ligand excluded by PLIP SO4.149: 2 residues within 4Å: Chain V: N.4, R.5 Ligand excluded by PLIP SO4.150: 3 residues within 4Å: Chain V: S.144, K.147, N.148 Ligand excluded by PLIP SO4.151: 4 residues within 4Å: Chain M: T.152 Chain V: G.150, D.151, T.152 Ligand excluded by PLIP SO4.155: 3 residues within 4Å: Chain W: P.161, S.162, S.163 Ligand excluded by PLIP SO4.156: 4 residues within 4Å: Chain C: R.123, R.127 Chain W: R.123, R.127 Ligand excluded by PLIP SO4.161: 6 residues within 4Å: Chain X: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.164 Ligand excluded by PLIP SO4.162: 2 residues within 4Å: Chain X: S.144, N.148 Ligand excluded by PLIP SO4.163: 3 residues within 4Å: Chain X: P.161, S.162, S.163 Ligand excluded by PLIP

30 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: R.58, H.59, N.62, L.124, R.127, I.128, E.131 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain A: Q.77, K.78 Chain B: Q.77, K.78 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain C: R.58, H.59, N.62, L.124, R.127, I.128, E.131 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain C: Q.77, K.78 Chain D: Q.77, K.78 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain D: R.58, H.59, N.62, R.127, E.131 Ligand excluded by PLIP GOL.28: 3 residues within 4Å: Chain D: P.89, V.90, K.147 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain E: Q.77, K.78 Chain F: Q.77, K.78 Ligand excluded by PLIP GOL.47: 5 residues within 4Å: Chain G: R.58, H.59, N.62, R.127, E.131 Ligand excluded by PLIP GOL.48: 4 residues within 4Å: Chain G: Q.77, K.78 Chain H: Q.77, K.78 Ligand excluded by PLIP GOL.55: 6 residues within 4Å: Chain H: R.58, H.59, N.62, L.124, R.127, E.131 Ligand excluded by PLIP GOL.61: 7 residues within 4Å: Chain I: R.58, H.59, N.62, L.124, R.127, I.128, E.131 Ligand excluded by PLIP GOL.68: 4 residues within 4Å: Chain I: Q.77, K.78 Chain J: Q.77, K.78 Ligand excluded by PLIP GOL.74: 7 residues within 4Å: Chain K: R.58, H.59, N.62, L.124, R.127, I.128, E.131 Ligand excluded by PLIP GOL.75: 4 residues within 4Å: Chain K: Q.77, K.78 Chain L: Q.77, K.78 Ligand excluded by PLIP GOL.82: 5 residues within 4Å: Chain L: R.58, H.59, N.62, R.127, E.131 Ligand excluded by PLIP GOL.83: 3 residues within 4Å: Chain L: P.89, V.90, K.147 Ligand excluded by PLIP GOL.90: 4 residues within 4Å: Chain M: Q.77, K.78 Chain N: Q.77, K.78 Ligand excluded by PLIP GOL.102: 5 residues within 4Å: Chain O: R.58, H.59, N.62, R.127, E.131 Ligand excluded by PLIP GOL.103: 4 residues within 4Å: Chain O: Q.77, K.78 Chain P: Q.77, K.78 Ligand excluded by PLIP GOL.110: 6 residues within 4Å: Chain P: R.58, H.59, N.62, L.124, R.127, E.131 Ligand excluded by PLIP GOL.116: 7 residues within 4Å: Chain Q: R.58, H.59, N.62, L.124, R.127, I.128, E.131 Ligand excluded by PLIP GOL.123: 4 residues within 4Å: Chain Q: Q.77, K.78 Chain R: Q.77, K.78 Ligand excluded by PLIP GOL.129: 7 residues within 4Å: Chain S: R.58, H.59, N.62, L.124, R.127, I.128, E.131 Ligand excluded by PLIP GOL.130: 4 residues within 4Å: Chain S: Q.77, K.78 Chain T: Q.77, K.78 Ligand excluded by PLIP GOL.137: 5 residues within 4Å: Chain T: R.58, H.59, N.62, R.127, E.131 Ligand excluded by PLIP GOL.138: 3 residues within 4Å: Chain T: P.89, V.90, K.147 Ligand excluded by PLIP GOL.145: 4 residues within 4Å: Chain U: Q.77, K.78 Chain V: Q.77, K.78 Ligand excluded by PLIP GOL.157: 5 residues within 4Å: Chain W: R.58, H.59, N.62, R.127, E.131 Ligand excluded by PLIP GOL.158: 4 residues within 4Å: Chain W: Q.77, K.78 Chain X: Q.77, K.78 Ligand excluded by PLIP GOL.165: 6 residues within 4Å: Chain X: R.58, H.59, N.62, L.124, R.127, E.131 Ligand excluded by PLIP

3 x 3PY: 3-HYDROXYPYRUVIC ACID(Non-covalent)

3PY.11: 5 residues within 4Å: Chain B: H.59, N.62, L.124, R.127, E.131 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.131 3PY.66: 5 residues within 4Å: Chain J: H.59, N.62, L.124, R.127, E.131 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:E.131 3PY.121: 5 residues within 4Å: Chain R: H.59, N.62, L.124, R.127, E.131 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:E.131

12 x FEC: 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX(Covalent)

FEC.12: 24 residues within 4Å: Chain A: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169 Chain B: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 Ligands: SO4.9 21 PLIP interactions: 9 interactions with chain A, 12 interactions with chain B, Hydrophobic interactions: A:L.24, A:I.27, A:M.31, A:E.61, B:I.27, B:M.31, B:M.57, B:E.61 Hydrogen bonds: A:Y.35, B:S.168, B:S.168, B:S.168, B:K.169 Water bridges: A:R.20, B:R.20 Salt bridges: A:R.20, A:K.169, A:K.169, B:R.20, B:K.50, B:K.169 FEC.26: 22 residues within 4Å: Chain C: R.20, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169 Chain D: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 21 PLIP interactions: 12 interactions with chain D, 9 interactions with chain C, Hydrophobic interactions: D:I.27, D:M.31, D:M.57, D:E.61, C:I.27, C:I.27, C:M.31, C:I.54, C:E.61 Hydrogen bonds: D:S.168, D:S.168, D:K.169, C:Y.35 Water bridges: D:R.20, D:N.32, D:T.164 Salt bridges: D:R.20, D:K.50, C:R.20, C:K.169, C:K.169 FEC.42: 24 residues within 4Å: Chain E: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169 Chain F: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 Ligands: SO4.38 21 PLIP interactions: 9 interactions with chain E, 12 interactions with chain F, Hydrophobic interactions: E:L.24, E:I.27, E:M.31, E:I.54, E:E.61, F:I.27, F:M.31, F:E.61 Hydrogen bonds: E:Y.35, F:Y.35, F:S.168, F:S.168, F:K.169 Salt bridges: E:R.20, E:K.169, E:K.169, F:R.20, F:K.50, F:K.169 Water bridges: F:R.20, F:N.32 FEC.54: 24 residues within 4Å: Chain G: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169 Chain H: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 Ligands: SO4.51 18 PLIP interactions: 8 interactions with chain G, 10 interactions with chain H, Hydrophobic interactions: G:L.24, G:M.31, G:I.54, G:E.61, H:I.27, H:M.31, H:M.57, H:E.61 Hydrogen bonds: G:Y.35, H:S.168, H:S.168, H:K.169 Water bridges: G:K.169, H:T.164 Salt bridges: G:R.20, G:K.169, H:R.20, H:K.50 FEC.67: 24 residues within 4Å: Chain I: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169 Chain J: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 Ligands: SO4.64 21 PLIP interactions: 9 interactions with chain I, 12 interactions with chain J, Hydrophobic interactions: I:L.24, I:I.27, I:M.31, I:E.61, J:I.27, J:M.31, J:M.57, J:E.61 Hydrogen bonds: I:Y.35, J:S.168, J:S.168, J:S.168, J:K.169 Water bridges: I:R.20, J:R.20 Salt bridges: I:R.20, I:K.169, I:K.169, J:R.20, J:K.50, J:K.169 FEC.81: 22 residues within 4Å: Chain K: R.20, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169 Chain L: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 21 PLIP interactions: 9 interactions with chain K, 12 interactions with chain L, Hydrophobic interactions: K:I.27, K:I.27, K:M.31, K:I.54, K:E.61, L:I.27, L:M.31, L:M.57, L:E.61 Hydrogen bonds: K:Y.35, L:Y.35, L:S.168, L:S.168, L:K.169 Salt bridges: K:R.20, K:K.169, K:K.169, L:R.20, L:K.50 Water bridges: L:R.20, L:N.32 FEC.97: 24 residues within 4Å: Chain M: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169 Chain N: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 Ligands: SO4.93 22 PLIP interactions: 12 interactions with chain N, 10 interactions with chain M, Hydrophobic interactions: N:I.27, N:M.31, N:E.61, M:L.24, M:I.27, M:M.31, M:I.54, M:E.61 Hydrogen bonds: N:Y.35, N:S.168, N:S.168, N:K.169, M:Y.35, M:Y.35 Water bridges: N:R.20, N:N.32 Salt bridges: N:R.20, N:K.50, N:K.169, M:R.20, M:K.169, M:K.169 FEC.109: 24 residues within 4Å: Chain O: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169 Chain P: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 Ligands: SO4.106 20 PLIP interactions: 10 interactions with chain O, 10 interactions with chain P, Hydrophobic interactions: O:L.24, O:M.31, O:I.54, O:E.61, P:I.27, P:M.31, P:M.57, P:E.61 Hydrogen bonds: O:Y.35, O:Y.35, P:Y.35, P:S.168, P:S.168, P:K.169 Water bridges: O:K.169, O:K.169 Salt bridges: O:R.20, O:K.169, P:R.20, P:K.50 FEC.122: 24 residues within 4Å: Chain Q: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169 Chain R: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 Ligands: SO4.119 21 PLIP interactions: 12 interactions with chain R, 9 interactions with chain Q, Hydrophobic interactions: R:I.27, R:M.31, R:M.57, R:E.61, Q:L.24, Q:I.27, Q:M.31, Q:E.61 Hydrogen bonds: R:Y.35, R:S.168, R:S.168, R:K.169, Q:Y.35 Water bridges: R:R.20, Q:R.20 Salt bridges: R:R.20, R:K.50, R:K.169, Q:R.20, Q:K.169, Q:K.169 FEC.136: 22 residues within 4Å: Chain S: R.20, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169 Chain T: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 22 PLIP interactions: 12 interactions with chain T, 10 interactions with chain S, Hydrophobic interactions: T:I.27, T:M.31, T:M.57, T:E.61, S:I.27, S:I.27, S:M.31, S:I.54, S:E.61 Hydrogen bonds: T:Y.35, T:S.168, T:S.168, T:K.169, S:Y.35, S:Y.35 Water bridges: T:R.20, T:N.32 Salt bridges: T:R.20, T:K.50, S:R.20, S:K.169, S:K.169 FEC.152: 24 residues within 4Å: Chain U: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169 Chain V: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 Ligands: SO4.148 22 PLIP interactions: 10 interactions with chain U, 12 interactions with chain V, Hydrophobic interactions: U:L.24, U:I.27, U:M.31, U:I.54, U:E.61, V:I.27, V:M.31, V:E.61 Hydrogen bonds: U:Y.35, U:Y.35, V:Y.35, V:S.168, V:S.168, V:K.169 Salt bridges: U:R.20, U:K.169, U:K.169, V:R.20, V:K.50, V:K.169 Water bridges: V:R.20, V:N.32 FEC.164: 24 residues within 4Å: Chain W: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169 Chain X: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 Ligands: SO4.161 19 PLIP interactions: 10 interactions with chain X, 9 interactions with chain W, Hydrophobic interactions: X:I.27, X:M.31, X:M.57, X:E.61, W:L.24, W:M.31, W:I.54, W:E.61 Hydrogen bonds: X:Y.35, X:S.168, X:S.168, X:K.169, W:Y.35 Salt bridges: X:R.20, X:K.50, W:R.20, W:K.169 Water bridges: W:K.169, W:K.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Macedo, S. et al., The nature of the di-iron site in the bacterioferritin fromDesulfovibrio desulfuricans. NAT.STRUCT.BIOL. (2003)

Release Date

2003-04-01

Peptides

bacterioferritin: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

E
K

F
L

G
O

H
P

I
C

J
D

K
E

L
F

M
K

N
L

O
O

P
P

Q
C

R
D

S
E

T
F

U
K

V
L

W
O

X
P

bacterioferritin

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