SMTL ID : 8qm3.1

formaldehyde-inhibited [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 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: 23 residues within 4Å: Chain A: A.230, P.231, S.232, I.268, A.272, C.299, C.300, 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, FOR.7, FOR.13, CL.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.232, A:Q.325, A:K.358 Metal complexes: A:C.503 402.19: 23 residues within 4Å: Chain B: A.230, P.231, S.232, I.268, A.272, C.299, C.300, 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: SF4.20, FOR.26, FOR.31, CL.32 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.232, B:Q.325, B:K.358 Metal complexes: B:C.503

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

SF4.2: 15 residues within 4Å: Chain A: C.193, C.300, P.301, G.302, P.354, C.355, S.357, K.358, M.497, A.498, C.499, C.503, G.506, G.507 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 SF4.20: 16 residues within 4Å: Chain B: C.193, C.300, P.301, G.302, P.354, C.355, S.357, K.358, M.497, A.498, C.499, G.502, C.503, G.506, G.507 Ligands: 402.19 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.300, B:C.355, B:C.499, B:C.503 SF4.21: 14 residues within 4Å: Chain B: 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 B, Metal complexes: B:C.157, B:C.190, B:C.193, B:C.196 SF4.22: 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 SF4.23: 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: 12 residues within 4Å: Chain A: A.32, L.33, C.34, F.35, N.40, K.45, C.46, E.47, I.48, 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.24: 12 residues within 4Å: Chain B: A.32, L.33, C.34, F.35, N.40, K.45, C.46, E.47, I.48, 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

10 x FOR: FORMYL GROUP(Non-covalent)(Covalent)

FOR.7: 6 residues within 4Å: Chain A: C.299, F.417, V.423, M.497 Ligands: 402.1, FOR.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.423 FOR.9: 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 FOR.11: 7 residues within 4Å: Chain A: T.275, E.279, T.297, S.298, C.299, S.319, V.423 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.298, A:C.299 FOR.12: 4 residues within 4Å: Chain A: R.136, S.137, C.184, D.186 No protein-ligand interaction detected (PLIP) FOR.13: 6 residues within 4Å: Chain A: C.299, C.300, V.423, M.497 Ligands: 402.1, FOR.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:C.300 FOR.25: 7 residues within 4Å: Chain B: T.275, E.279, T.297, S.298, C.299, S.319, V.423 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.298, B:C.299 FOR.26: 6 residues within 4Å: Chain B: C.299, C.300, V.423, M.497 Ligands: 402.19, FOR.31 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.423 FOR.28: 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 FOR.30: 5 residues within 4Å: Chain B: R.136, S.137, C.184, D.186, D.187 No protein-ligand interaction detected (PLIP) FOR.31: 6 residues within 4Å: Chain B: C.299, C.300, V.423, M.497 Ligands: 402.19, FOR.26 1 PLIP interactions: 1 interactions with chain B Water bridges: B:C.299

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 10 residues within 4Å: Chain A: K.223, K.333, K.345, N.346, V.347, F.348, G.371, L.372, R.373, D.376 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.223, A:K.333, A:V.347, A:R.373, A:D.376 GOL.10: 8 residues within 4Å: Chain A: R.103, R.104, E.105, N.106, C.107, L.110, K.111, I.114 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.107, A:K.111, A:K.111 GOL.27: 5 residues within 4Å: Chain B: K.446, R.449, G.450, K.524 Ligands: CL.38 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.452 GOL.29: 9 residues within 4Å: Chain B: K.223, K.333, K.345, N.346, V.347, F.348, L.372, R.373, D.376 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.223, B:V.347, B:R.373 Water bridges: B:K.333, B:P.344, B:D.376

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

CL.14: 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.17: 4 residues within 4Å: Chain A: R.364, P.365, Q.366, F.570 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain A: K.264, F.266, D.404, P.405, A.406 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: 402.19 Ligand excluded by PLIP CL.36: 4 residues within 4Å: Chain B: R.364, P.365, Q.366, F.570 Ligand excluded by PLIP CL.37: 5 residues within 4Å: Chain B: K.264, F.266, D.404, P.405, A.406 Ligand excluded by PLIP CL.38: 5 residues within 4Å: Chain A: L.65 Chain B: G.450, L.451, K.524 Ligands: GOL.27 Ligand excluded by PLIP

5 x MG: MAGNESIUM ION(Non-covalent)

MG.15: 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.3, H2O.4, H2O.7, H2O.8, H2O.9 MG.16: 3 residues within 4Å: Chain A: N.40, D.42, D.63 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.42, H2O.4, H2O.5, H2O.9, H2O.30 MG.33: 1 residues within 4Å: Chain B: N.309 No protein-ligand interaction detected (PLIP) MG.34: 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.21, H2O.26, H2O.26, H2O.31 MG.35: 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.22, H2O.23, H2O.28, H2O.29, H2O.29

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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