SMTL ID : 9er9.1

Hydrogenase-1 Ni-R 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: 13 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, P.224, I.243 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.187, A:C.190, A:C.215, A:C.221 SF4.14: 12 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, P.224, 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.15: 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: 10 residues within 4Å: Chain A: 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 SF3.16: 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, SF3.16

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.12: 1 residues within 4Å: Chain B: R.183 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain C: T.114, W.118, C.120, G.256 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain C: D.173, R.174 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: A.194, H.195, A.198, E.200 Chain C: D.188, R.193 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:A.194, A:H.195, C:D.188, C:R.193 Water bridges: A:Y.214, C:R.193, C:R.193 GOL.6: 8 residues within 4Å: Chain A: I.12, H.13, Y.44, D.46, S.90, K.98 Chain B: P.23, H.30 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.13, A:Y.44, A:Y.44, A:S.90, B:H.30 Water bridges: A:D.46, A:S.90 GOL.18: 6 residues within 4Å: Chain A: D.188, R.193 Chain C: A.194, H.195, A.198, E.200 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:R.193, C:A.194, C:H.195 Water bridges: A:Q.184, A:R.193, A:R.193, C:Y.214 GOL.19: 8 residues within 4Å: Chain C: I.12, H.13, Y.44, D.46, S.90, K.98 Chain D: P.23, H.30 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:H.13, C:S.90, C:S.90, C:K.98, D:H.30 Water bridges: C:Y.44

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

SO4.7: 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

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

FCO.8: 13 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.9 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.21: 13 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.22 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.9: 5 residues within 4Å: Chain B: C.76, C.79, C.576, C.579 Ligands: FCO.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.76, B:C.79, B:C.576, B:C.579 NI.22: 5 residues within 4Å: Chain D: C.76, C.79, C.576, C.579 Ligands: FCO.21 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.76, D:C.79, D:C.576, D:C.579

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 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.10, H2O.11, H2O.11 MG.23: 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.38, H2O.38, H2O.39

2 x 01: 2-[[2-[2-[2-[bis(2-hydroxy-2-oxoethyl)amino]phenoxy]ethoxy]phenyl]-(2-hydroxy-2-oxoethyl)amino]ethanoic acid

01.11: 10 residues within 4Å: Chain B: Q.150, S.151, L.152, S.153, S.154 Chain D: R.143, P.160, G.161, F.164 Ligands: EU.25 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:P.160, D:F.164, D:F.164 Salt bridges: D:R.143, D:R.143 pi-Cation interactions: D:R.143 01.24: 10 residues within 4Å: Chain B: R.143, P.160, G.161, F.164 Chain D: Q.150, S.151, L.152, S.153, S.154 Ligands: EU.13 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain B Hydrogen bonds: D:Q.150 Hydrophobic interactions: B:P.160, B:F.164 Water bridges: B:R.143 Salt bridges: B:R.143, B:R.143 pi-Cation interactions: B:R.143

2 x EU: EUROPIUM ION(Non-functional Binders)

EU.13: 1 residues within 4Å: Ligands: 01.24 No protein-ligand interaction detected (PLIP) EU.25: 1 residues within 4Å: Ligands: 01.11 No protein-ligand interaction detected (PLIP)

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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