SMTL ID : 6hac.1

Crystal structure of [Fe]-hydrogenase (Hmd) holoenzyme from Methanococcus aeolicus (open form)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

FE9.1: 26 residues within 4Å: Chain A: L.6, G.7, A.8, G.9, C.10, S.13, 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 17 PLIP interactions: 16 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: 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 Water bridges: A:S.42 Salt bridges: A:D.64, A:D.135 Metal complexes: A:C.176, H2O.2 FE9.6: 26 residues within 4Å: Chain B: L.6, G.7, A.8, G.9, C.10, S.13, 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 17 PLIP interactions: 16 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: 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.42 Salt bridges: B:D.64, B:D.135 Metal complexes: B:C.176, H2O.6

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 6 residues within 4Å: Chain A: C.17, I.19 Chain B: L.275, S.320, M.321, F.323 No protein-ligand interaction detected (PLIP) 1PE.7: 6 residues within 4Å: Chain A: L.275, S.320, M.321, F.323 Chain B: C.17, I.19 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: D.77, K.107 4 PLIP interactions: 4 interactions with chain A Water bridges: A:I.75, A:D.77, A:D.77, A:E.78 GOL.4: 6 residues within 4Å: Chain A: L.294, E.295, R.298 Chain B: L.294, R.298 Ligands: GOL.9 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.298, A:R.298, A:R.298 GOL.8: 2 residues within 4Å: Chain B: D.77, K.107 3 PLIP interactions: 3 interactions with chain B Water bridges: B:I.75, B:D.77, B:D.77 GOL.9: 6 residues within 4Å: Chain A: L.294, R.298 Chain B: L.294, E.295, R.298 Ligands: GOL.4 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.298, B:R.298, A:R.298

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

NA.5: 5 residues within 4Å: Chain A: P.325, L.326, S.327, E.328, L.329 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.325, A:E.328, A:L.329 NA.10: 5 residues within 4Å: Chain B: P.325, L.326, S.327, E.328, L.329 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.325, B:E.328, B:L.329

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
A

5,10-methenyltetrahydromethanopterin hydrogenase

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