SMTL ID : 8pvm.1

formaldehyde-inhibited [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant C299D

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-dimer

Ligands

2 x 402: dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)(Non-covalent)

402.1: 20 residues within 4Å: Chain A: A.230, P.231, S.232, I.268, A.272, D.299, S.323, P.324, Q.325, M.353, P.354, C.355, K.358, F.417, G.418, V.423, M.497, C.503 Ligands: SF4.2, CL.15 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.232, A:D.299, A:Q.325 Salt bridges: A:D.299 Metal complexes: A:C.503 402.16: 21 residues within 4Å: Chain B: A.230, P.231, S.232, I.268, A.272, D.299, C.300, S.323, P.324, Q.325, M.353, P.354, C.355, K.358, F.417, G.418, M.497, C.503 Ligands: SF4.17, 74C.22, CL.32 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.232, B:D.299, B:Q.325 Metal complexes: B:C.503

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

SF4.2: 10 residues within 4Å: Chain A: C.300, P.301, C.355, K.358, M.497, A.498, C.499, C.503, G.506 Ligands: 402.1 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.300, A:C.355, A:C.499, A:C.503 SF4.3: 14 residues within 4Å: Chain A: L.140, C.157, T.161, T.163, A.165, M.166, F.185, C.190, L.191, L.192, C.193, G.194, Q.195, C.196 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.157, A:C.190, A:C.193, A:C.196 SF4.4: 13 residues within 4Å: Chain A: C.147, L.148, L.149, C.150, G.151, R.152, C.153, I.177, C.200, P.201, V.202, A.204, L.205 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.147, A:C.150, A:C.153, A:C.200 SF4.5: 14 residues within 4Å: Chain A: H.94, E.95, F.96, K.97, C.98, C.101, R.103, R.104, C.107, F.109, L.110, K.146, V.202, A.203 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.94, A:C.98, A:C.101, A:C.107 SF4.17: 10 residues within 4Å: Chain B: C.300, P.301, C.355, K.358, M.497, A.498, C.499, C.503, G.506 Ligands: 402.16 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.300, B:C.355, B:C.499, B:C.503 SF4.18: 12 residues within 4Å: Chain B: L.140, C.157, T.161, T.163, M.166, C.190, L.191, L.192, C.193, G.194, Q.195, C.196 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.157, B:C.190, B:C.193, B:C.196 SF4.19: 13 residues within 4Å: Chain B: C.147, L.148, L.149, C.150, G.151, R.152, C.153, I.177, C.200, P.201, V.202, A.204, L.205 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.147, B:C.150, B:C.153, B:C.200 SF4.20: 14 residues within 4Å: Chain B: H.94, E.95, F.96, K.97, C.98, C.101, R.103, R.104, C.107, F.109, L.110, K.146, V.202, A.203 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:H.94, B:C.98, B:C.101, B:C.107

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.6: 11 residues within 4Å: Chain A: A.32, L.33, C.34, F.35, N.40, K.45, C.46, E.47, C.49, T.60, C.62 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.34, A:C.46, A:C.49, A:C.62 FES.21: 11 residues within 4Å: Chain B: A.32, L.33, C.34, F.35, N.40, K.45, C.46, E.47, C.49, T.60, C.62 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.34, B:C.46, B:C.49, B:C.62

3 x 74C: methyl radical(Covalent)(Non-covalent)

74C.7: 4 residues within 4Å: Chain A: N.37, N.38, C.39, K.159 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.159 74C.22: 4 residues within 4Å: Chain B: D.299, F.417, V.423 Ligands: 402.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.299, B:F.417, B:V.423 74C.23: 4 residues within 4Å: Chain B: N.37, N.38, C.39, K.159 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.159

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain A: K.223, K.333, K.345, V.347, F.348, L.372, R.373, D.376 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.333, A:K.345, A:R.373 GOL.9: 7 residues within 4Å: Chain A: R.103, R.104, E.105, N.106, C.107, L.110, K.111 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.104, A:C.107, A:K.111 GOL.24: 8 residues within 4Å: Chain B: K.223, K.333, K.345, V.347, F.348, L.372, R.373, D.376 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.373, B:R.373 Water bridges: B:K.333, B:K.333, B:D.376 GOL.25: 8 residues within 4Å: Chain B: R.103, R.104, E.105, N.106, C.107, L.110, K.111, I.114 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.104, B:C.107, B:C.107

2 x FOR: FORMYL GROUP(Covalent)

FOR.10: 4 residues within 4Å: Chain A: R.136, C.184, D.186, D.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.186 FOR.26: 4 residues within 4Å: Chain B: R.136, C.184, D.186, D.187 No protein-ligand interaction detected (PLIP)

5 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 2 residues within 4Å: Chain A: N.40, D.42 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.42, H2O.6, H2O.7, H2O.11, H2O.13 MG.12: 1 residues within 4Å: Chain A: L.218 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:L.218, H2O.4, H2O.6, H2O.8, H2O.9, H2O.11 MG.27: 2 residues within 4Å: Chain B: N.40, D.42 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.42, H2O.26, H2O.30, H2O.32, H2O.36 MG.28: 1 residues within 4Å: Chain B: L.218 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:L.218, H2O.27, H2O.30, H2O.31, H2O.32, H2O.32 MG.29: 1 residues within 4Å: Chain B: N.309 No protein-ligand interaction detected (PLIP)

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

CL.13: 3 residues within 4Å: Chain A: R.364, P.365, Q.366 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: N.106, R.382, P.510, H.511 Ligand excluded by PLIP CL.15: 7 residues within 4Å: Chain A: A.230, P.231, S.232, P.354, G.418, C.503 Ligands: 402.1 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain B: R.364, P.365, Q.366 Ligand excluded by PLIP CL.31: 5 residues within 4Å: Chain B: N.106, L.240, R.382, P.510, H.511 Ligand excluded by PLIP CL.32: 7 residues within 4Å: Chain B: A.230, P.231, S.232, P.354, G.418, C.503 Ligands: 402.16 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duan, J. et al., Insights into the Molecular Mechanism of Formaldehyde Inhibition of [FeFe]-Hydrogenases. J.Am.Chem.Soc. (2023)

Release Date

2023-11-29

Peptides

Iron hydrogenase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Iron hydrogenase 1

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