SMTL ID : 6hae.1

Crystal structure of [Fe]-hydrogenase (Hmd) from Methanococcus aeolicus in complex with FeGP cofactor and methenyl-tetrahydromethanopterin (close form B)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: I.19, T.20, N.21, A.93, E.94, R.101, M.208 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.21 GOL.16: 4 residues within 4Å: Chain B: G.217, Y.218, A.243, N.244 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.244, B:N.244 Water bridges: B:A.243

2 x E4M: 1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol(Non-covalent)

E4M.2: 19 residues within 4Å: Chain A: S.13, H.14, C.17, K.113, P.114, P.150, K.151, C.176, G.203, C.250, D.251, M.252, S.254 Chain B: P.278, F.281, T.317, S.320, M.321 Ligands: FE9.15 16 PLIP interactions: 5 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:F.281 Hydrogen bonds: B:T.317, B:S.320, A:P.114, A:K.151, A:C.250, A:M.252, A:S.254 Water bridges: B:G.276, B:G.276, A:K.151, A:K.151 Salt bridges: A:K.113, A:K.151, A:K.151, A:K.151 E4M.17: 19 residues within 4Å: Chain A: P.278, F.281, T.317, S.320, M.321 Chain B: S.13, H.14, C.17, K.113, P.114, P.150, K.151, C.176, G.203, C.250, D.251, M.252, S.254 Ligands: FE9.30 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:P.114, B:K.151, B:C.250, B:M.252, B:S.254, A:T.317, A:S.320 Water bridges: B:K.113, B:K.113, B:K.113, B:K.151, A:G.276 Salt bridges: B:K.113, B:K.151, B:K.151 Hydrophobic interactions: A:F.281

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: V.54, D.55, E.56 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.55, A:E.56 Water bridges: A:D.55 NA.18: 3 residues within 4Å: Chain B: V.54, D.55, E.56 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.55, B:E.56 Water bridges: B:D.55, B:D.55

15 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.4: 4 residues within 4Å: Chain A: G.152, G.153, I.178, K.182 No protein-ligand interaction detected (PLIP) SCN.5: 4 residues within 4Å: Chain A: N.196, S.220, E.222 Ligands: SCN.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.220 SCN.6: 3 residues within 4Å: Chain A: E.225, Y.228, K.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.232 Water bridges: A:Y.228 SCN.7: 4 residues within 4Å: Chain A: E.193, L.195, N.196 Ligands: SCN.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.196 SCN.8: 4 residues within 4Å: Chain A: K.232, T.237, A.238, F.239 No protein-ligand interaction detected (PLIP) SCN.9: 2 residues within 4Å: Chain A: L.129, K.130 No protein-ligand interaction detected (PLIP) SCN.10: 4 residues within 4Å: Chain A: I.34, H.52, V.127, G.128 No protein-ligand interaction detected (PLIP) SCN.11: 5 residues within 4Å: Chain A: P.71, I.74, D.110, S.111, P.112 No protein-ligand interaction detected (PLIP) SCN.19: 4 residues within 4Å: Chain B: E.193, L.195, N.196, Y.218 No protein-ligand interaction detected (PLIP) SCN.20: 5 residues within 4Å: Chain A: V.336, E.339, H.340 Chain B: S.266, P.325 No protein-ligand interaction detected (PLIP) SCN.21: 3 residues within 4Å: Chain B: S.220, E.221, E.222 No protein-ligand interaction detected (PLIP) SCN.22: 4 residues within 4Å: Chain B: G.152, G.153, I.178, K.182 No protein-ligand interaction detected (PLIP) SCN.23: 4 residues within 4Å: Chain A: R.12, S.13, A.16 Chain B: L.275 No protein-ligand interaction detected (PLIP) SCN.24: 3 residues within 4Å: Chain B: R.136, E.140, A.165 No protein-ligand interaction detected (PLIP) SCN.25: 3 residues within 4Å: Chain B: K.232, T.237, A.238 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 3 residues within 4Å: Chain A: K.151, G.153 Chain B: F.281 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain A: F.281 Chain B: K.151, G.153 Ligand excluded by PLIP

4 x K: POTASSIUM ION(Non-covalent)

K.13: 5 residues within 4Å: Chain A: L.50, L.51, V.54, D.55, I.57 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:L.51, A:V.54, A:I.57, H2O.6, H2O.8 K.14: 3 residues within 4Å: Chain A: E.125, K.130, V.131 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.125, H2O.11 K.27: 5 residues within 4Å: Chain B: L.50, L.51, V.54, D.55, I.57 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:L.51, B:V.54, B:I.57, H2O.18, H2O.19 K.28: 3 residues within 4Å: Chain B: D.164, I.166, R.192 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.164, H2O.12

2 x FE9: iron-guanylyl pyridinol cofactor(Non-covalent)

FE9.15: 28 residues within 4Å: Chain A: L.6, G.7, A.8, G.9, C.10, S.13, H.14, S.63, D.64, P.65, P.114, P.115, C.118, D.135, W.148, L.149, P.150, I.158, A.175, C.176, T.177, H.201, P.202, G.203, C.204, V.205, P.206 Ligands: E4M.2 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:W.148, A:W.148, A:A.175, A:T.177 Hydrogen bonds: A:A.8, A:G.9, A:G.9, A:C.10, A:C.10, A:S.63, A:C.176, A:G.203, A:C.204 Salt bridges: A:D.64, A:D.135 Metal complexes: A:C.176 FE9.30: 28 residues within 4Å: Chain B: L.6, G.7, A.8, G.9, C.10, S.13, H.14, S.63, D.64, P.65, P.114, P.115, C.118, D.135, W.148, L.149, P.150, I.158, A.175, C.176, T.177, H.201, P.202, G.203, C.204, V.205, P.206 Ligands: E4M.17 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:W.148, B:W.148, B:A.175, B:T.177 Hydrogen bonds: B:A.8, B:G.9, B:G.9, B:C.10, B:C.10, B:S.63, B:C.176, B:G.203, B:C.204 Water bridges: B:S.133, B:D.135 Salt bridges: B:D.64, B:D.135 Metal complexes: B:C.176

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.29: 6 residues within 4Å: Chain B: S.23, R.24, E.27, M.208, K.209, G.210 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.209 Hydrogen bonds: B:G.210 Water bridges: B:R.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, G. et al., The atomic-resolution crystal structure of activated [Fe]-hydrogenase. Nat Catal (2019)

Release Date

2019-08-28

Peptides

5,10-methenyltetrahydromethanopterin hydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
K

5,10-methenyltetrahydromethanopterin hydrogenase

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