SMTL ID : 9er7.1

Hydrogenase-1 Ni-SCO state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-2-2-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: I.186, H.187, C.190, R.192, R.193, F.196, C.215, L.216, Y.217, C.221, G.223, I.243 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.187, A:C.190, A:C.215, A:C.221 SF4.12: 11 residues within 4Å: Chain C: H.187, C.190, R.192, R.193, F.196, C.215, L.216, Y.217, C.221, G.223, I.243 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.187, C:C.190, C:C.215, C:C.221

2 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.2: 10 residues within 4Å: Chain A: T.226, N.228, C.230, W.235, P.242, C.249, L.250, G.251, C.252 Chain B: K.226 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.230, A:C.249, A:C.252 F3S.13: 10 residues within 4Å: Chain C: T.226, N.228, C.230, W.235, P.242, C.249, L.250, G.251, C.252 Chain D: K.226 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.230, C:C.249, C:C.252

2 x SF3: FE4-S3 CLUSTER(Non-covalent)

SF3.3: 11 residues within 4Å: Chain A: E.16, C.17, T.18, C.19, C.20, T.114, C.115, C.120, G.148, C.149 Chain B: R.74 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Salt bridges: A:E.76 Metal complexes: A:C.17, A:C.19, A:C.19, A:C.20, A:C.115, A:C.120, A:C.149, SF3.3 SF3.14: 10 residues within 4Å: Chain C: C.17, T.18, C.19, C.20, T.114, C.115, C.120, G.148, C.149 Chain D: R.74 9 PLIP interactions: 8 interactions with chain C, 1 Ligand-Ligand interactions Salt bridges: C:E.76 Metal complexes: C:C.17, C:C.19, C:C.19, C:C.20, C:C.115, C:C.120, C:C.149, SF3.14

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

CL.4: 4 residues within 4Å: Chain A: T.114, W.118, C.120, G.256 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: I.12, H.13, D.46, K.98 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain C: T.114, W.118, G.119, C.120, G.256 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain C: I.12, H.13, D.46, K.98 Ligand excluded by PLIP

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

SO4.6: 5 residues within 4Å: Chain A: R.211 Chain B: G.480, N.481, L.482, A.483 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.481, B:L.482, B:A.483 Salt bridges: A:R.211 SO4.17: 6 residues within 4Å: Chain A: K.212, Y.214 Chain B: S.246, G.247 Chain C: G.183, Q.184 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:Y.214, C:Q.184, B:S.246 Salt bridges: A:K.212 SO4.22: 6 residues within 4Å: Chain A: G.183, Q.184 Chain C: K.212, Y.214 Chain D: S.246, G.247 6 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: C:Y.214, A:G.183, A:Q.184, D:S.246 Salt bridges: C:K.212 Water bridges: A:D.188

2 x FCO: CARBONMONOXIDE-(DICYANO) IRON(Non-covalent)

FCO.7: 14 residues within 4Å: Chain B: C.79, V.82, H.83, A.507, P.508, R.509, L.512, V.530, P.531, T.532, C.576, C.579 Ligands: NI.8, CMO.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.509, B:R.509, B:T.532 Metal complexes: B:C.79, B:C.579 FCO.18: 14 residues within 4Å: Chain D: C.79, V.82, H.83, A.507, P.508, R.509, L.512, V.530, P.531, T.532, C.576, C.579 Ligands: NI.19, CMO.21 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.509, D:R.509, D:T.532 Metal complexes: D:C.79, D:C.579

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

NI.8: 6 residues within 4Å: Chain B: C.76, C.79, C.576, C.579 Ligands: FCO.7, CMO.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:C.76, B:C.79, B:C.576, B:C.579, CMO.10 NI.19: 6 residues within 4Å: Chain D: C.76, C.79, C.576, C.579 Ligands: FCO.18, CMO.21 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:C.76, D:C.79, D:C.576, D:C.579, CMO.21

2 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain B: E.57, C.528, H.582 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.57, B:C.528, B:H.582, H2O.9, H2O.9, H2O.9 MG.20: 3 residues within 4Å: Chain D: E.57, C.528, H.582 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.57, D:C.528, D:H.582, H2O.35, H2O.35, H2O.35

2 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.10: 7 residues within 4Å: Chain B: C.76, V.78, C.79, R.509, C.576 Ligands: FCO.7, NI.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.79 CMO.21: 8 residues within 4Å: Chain D: C.76, V.78, C.79, R.509, C.576, C.579 Ligands: FCO.18, NI.19 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:C.79

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.11: 4 residues within 4Å: Chain A: Y.264, S.265 Chain B: R.66, E.491 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.66, B:R.66, B:E.491, A:S.265 Water bridges: B:W.490, B:W.490, B:E.491, A:Y.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carr, S.B. et al., Glutamate flick enables proton tunnelling during fast redox biocatalysis. To Be Published

Release Date

2025-04-02

Peptides

Hydrogenase-1 small chain: AC
Hydrogenase-1 large chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

C
T

B
L

D
M

Hydrogenase-1 small chain

Hydrogenase-1 large chain

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