SMTL ID : 6rp2.1

Threonine to Cysteine (T225C) variant of E coli hydrogenase-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 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.183, H.184, C.187, R.189, R.190, F.193, C.212, L.213, Y.214, C.218, G.220, I.240 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.184, A:C.187, A:C.212, A:C.218 SF4.11: 11 residues within 4Å: Chain C: H.184, C.187, R.189, R.190, F.193, C.212, L.213, Y.214, C.218, G.220, I.240 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.184, C:C.187, C:C.212, C:C.218

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

F3S.2: 10 residues within 4Å: Chain A: T.223, N.225, C.227, W.232, P.239, C.246, L.247, G.248, C.249 Chain B: K.226 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.227, A:C.246, A:C.249 F3S.12: 10 residues within 4Å: Chain C: T.223, N.225, C.227, W.232, P.239, C.246, L.247, G.248, C.249 Chain D: K.226 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.227, C:C.246, C:C.249

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

SF3.3: 10 residues within 4Å: Chain A: C.14, T.15, C.16, C.17, T.111, C.112, C.117, G.145, C.146 Chain B: R.74 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Salt bridges: A:E.73 Metal complexes: A:C.14, A:C.16, A:C.16, A:C.17, A:C.112, A:C.117, A:C.146, SF3.3 SF3.13: 12 residues within 4Å: Chain C: E.13, C.14, T.15, C.16, C.17, G.110, T.111, C.112, C.117, G.145, C.146 Chain D: R.74 9 PLIP interactions: 8 interactions with chain C, 1 Ligand-Ligand interactions Salt bridges: C:E.73 Metal complexes: C:C.14, C:C.16, C:C.16, C:C.17, C:C.112, C:C.117, C:C.146, SF3.13

2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.4: 12 residues within 4Å: Chain A: I.4, V.6, W.8, I.69, S.104, A.105, W.109, I.157, M.160, V.161, D.164, R.165 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.4, A:I.4, A:V.6, A:V.6, A:W.8, A:I.69, A:I.69, A:W.109, A:I.157, A:M.160, A:V.161 Hydrogen bonds: A:S.104 Water bridges: A:L.166 LMT.14: 10 residues within 4Å: Chain C: I.4, V.6, W.8, I.37, I.69, I.157, M.160, V.161, D.164, R.165 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.6, C:V.6, C:W.8, C:I.37, C:I.69, C:I.157, C:I.157, C:M.160, C:V.161

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

CL.5: 4 residues within 4Å: Chain A: T.111, W.115, C.117, G.253 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain C: T.111, W.115, C.117, G.253 Ligand excluded by PLIP

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

SO4.6: 5 residues within 4Å: Chain A: R.208 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:G.480, B:L.482, B:A.483 Salt bridges: A:R.208 SO4.19: 1 residues within 4Å: Chain D: R.394 2 PLIP interactions: 2 interactions with chain D Water bridges: D:R.394 Salt bridges: D:R.394

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

FCO.7: 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.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Hydrogen bonds: B:R.509, B:R.509, B:T.532 Metal complexes: B:C.579, H2O.25 FCO.16: 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.17 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Hydrogen bonds: D:R.509, D:R.509, D:T.532 Metal complexes: D:C.579, H2O.50

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

NI.8: 5 residues within 4Å: Chain B: C.76, C.79, C.576, C.579 Ligands: FCO.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.76, B:C.576, B:C.579, H2O.25 NI.17: 5 residues within 4Å: Chain D: C.76, C.79, C.576, C.579 Ligands: FCO.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.76, D:C.576, D:C.579, H2O.50

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.10, H2O.10, H2O.11 MG.18: 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.39, H2O.39, H2O.39

2 x LI: LITHIUM ION(Non-covalent)

LI.10: 1 residues within 4Å: Chain B: I.97 No protein-ligand interaction detected (PLIP) LI.20: 1 residues within 4Å: Chain D: I.97 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., Aerobic Photocatalytic H2Production by a [NiFe] Hydrogenase Engineered to Place a Silver Nanocluster in the Electron Relay. J.Am.Chem.Soc. (2020)

Release Date

2020-03-25

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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