SMTL ID : 1gx7.1

Best model of the electron transfer complex between cytochrome c3 and [Fe]-hydrogenase

Coordinates

PDB Format

Method

THEORETICAL MODEL

Oligo State

hetero-1-1-1-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: K.8, C.9, I.10, G.11, C.12, D.13, C.15, S.16, H.32, H.49, C.50, I.55 Ligands: HEC.11 5 PLIP interactions: 5 interactions with chain A, pi-Cation interactions: A:H.32 Metal complexes: A:C.9, A:C.12, A:C.15, A:C.50 SF4.2: 12 residues within 4Å: Chain A: V.2, Y.18, C.19, T.21, I.24, A.39, C.40, I.41, C.43, G.44, Q.45, C.46 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.19, A:C.40, A:C.43, A:C.46 SF4.3: 12 residues within 4Å: Chain A: C.43, C.153, P.154, C.208, K.211, M.350, A.351, C.352, G.355, C.356, G.359, G.360 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.153, A:C.208, A:C.352, A:C.356

1 x PDT: 1,3-PROPANEDITHIOL(Non-covalent)

PDT.4: 14 residues within 4Å: Chain A: A.83, P.177, M.206, K.211, F.270, G.271, M.350, C.356 Ligands: FE2.5, FE2.6, CYN.7, CYN.8, CMO.9, CMO.10 No protein-ligand interaction detected (PLIP)

2 x FE2: FE (II) ION(Non-covalent)

FE2.5: 10 residues within 4Å: Chain A: A.81, T.119, M.206, G.271 Ligands: PDT.4, FE2.6, CYN.7, CYN.8, CMO.9, CMO.10 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: CMO.10 FE2.6: 9 residues within 4Å: Chain A: T.119, M.206, G.271 Ligands: PDT.4, FE2.5, CYN.7, CYN.8, CMO.9, CMO.10 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: CMO.9

2 x CYN: CYANIDE ION(Non-covalent)

CYN.7: 10 residues within 4Å: Chain A: P.177, I.178, M.206, K.211 Ligands: PDT.4, FE2.5, FE2.6, CYN.8, CMO.9, CMO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.178, A:K.211 CYN.8: 13 residues within 4Å: Chain A: A.81, P.82, A.83, T.119, M.206, F.270, G.271 Ligands: PDT.4, FE2.5, FE2.6, CYN.7, CMO.9, CMO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.83, A:G.271

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

CMO.9: 9 residues within 4Å: Chain A: M.206, P.207, K.211 Ligands: PDT.4, FE2.5, FE2.6, CYN.7, CYN.8, CMO.10 No protein-ligand interaction detected (PLIP) CMO.10: 12 residues within 4Å: Chain A: P.82, T.119, M.206, A.267, F.270, G.271 Ligands: PDT.4, FE2.5, FE2.6, CYN.7, CYN.8, CMO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.119, A:T.119

4 x HEC: HEME C(Covalent)

HEC.11: 24 residues within 4Å: Chain A: I.10, C.12, M.28, P.51 Chain C: M.11, E.12, A.13, T.14, K.15, Q.16, V.18, Y.65, Y.66, M.69, H.70, C.79, V.80, L.97, T.98, C.100, C.105, H.106 Ligands: SF4.1, HEC.14 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:T.14, C:Q.16, C:V.18, C:V.18, C:V.80, C:T.98, A:P.51 Hydrogen bonds: C:A.13, C:T.14, C:T.14, C:T.14, C:K.15, C:Q.16, C:Y.65 pi-Stacking: C:Y.66, C:H.70, C:H.70 pi-Cation interactions: C:H.106 Metal complexes: C:H.70, C:H.106 HEC.12: 22 residues within 4Å: Chain C: H.34, H.35, P.36, V.37, N.38, K.40, D.42, R.44, K.45, C.46, T.48, C.51, H.52, S.61, A.62, H.67, V.68, M.69, T.74, K.75, F.76, S.78 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:V.37, C:T.48, C:V.68, C:V.68, C:V.68, C:F.76 Hydrogen bonds: C:N.38, C:N.38, C:A.62, C:K.75 Salt bridges: C:H.35, C:H.67, C:K.75 Metal complexes: C:H.35, C:H.52 HEC.13: 19 residues within 4Å: Chain C: P.2, K.3, A.4, L.9, M.11, F.20, H.22, H.25, K.26, V.28, C.30, C.33, H.34, Y.43, R.44, K.45, C.46, G.47 Ligands: HEC.14 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:A.4, C:L.9, C:F.20, C:F.20, C:F.20, C:H.25, C:K.26, C:Y.43 Hydrogen bonds: C:K.45, C:C.46, C:G.47, C:Y.65 Salt bridges: C:K.45 pi-Cation interactions: C:H.22, C:H.34 Metal complexes: C:H.22, C:H.34 HEC.14: 16 residues within 4Å: Chain C: V.19, F.20, N.21, S.23, T.24, H.25, V.28, C.33, M.69, C.79, C.82, H.83, K.104, C.105 Ligands: HEC.11, HEC.13 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:F.20, C:V.28 Hydrogen bonds: C:N.21, C:N.21, C:S.23, C:S.23, C:T.24 Salt bridges: C:H.25 Metal complexes: C:H.25, C:H.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Elantak, L. et al., The Cytochrome C(3)-[Fe]-Hydrogenase Electron-Transfer Complex: Structural Model by NMR Restrained Docking. FEBS Lett. (2003)

Release Date

2003-07-31

Peptides

PERIPLASMIC [FE] HYDROGENASE LARGE SUBUNIT: A
PERIPLASMIC [FE] HYDROGENASE SMALL SUBUNIT: B
CYTOCHROME C3: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
E

PERIPLASMIC [FE] HYDROGENASE LARGE SUBUNIT

PERIPLASMIC [FE] HYDROGENASE SMALL SUBUNIT

CYTOCHROME C3

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