SMTL ID : 1e08.1

Structural model of the [Fe]-Hydrogenase/cytochrome c553 complex combining NMR and soft-docking

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: I.4, K.8, C.9, I.10, G.11, C.12, D.13, C.15, S.16, H.32, H.49, C.50, I.55 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: F.1, V.2, Y.18, C.19, I.24, I.34, C.40, I.41, N.42, C.43, G.44, 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: 11 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 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.81, P.82, A.83, V.84, K.211, I.269, F.270, G.271 Ligands: FE2.5, FE2.6, CYN.7, CYN.8, CMO.9, CMO.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.81, A:V.84

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

FE2.5: 13 residues within 4Å: Chain A: P.82, A.83, T.119, A.123, A.267, I.269, F.270 Ligands: PDT.4, FE2.6, CYN.7, CYN.8, CMO.9, CMO.10 2 PLIP interactions: 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.1, CMO.10 FE2.6: 14 residues within 4Å: Chain A: P.82, A.83, T.119, A.123, P.177, A.267, I.269, F.270 Ligands: PDT.4, FE2.5, CYN.7, CYN.8, CMO.9, CMO.10 2 PLIP interactions: 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.1, CMO.9

2 x CYN: CYANIDE ION(Non-covalent)

CYN.7: 9 residues within 4Å: Chain A: A.123, P.177, F.270 Ligands: PDT.4, FE2.5, FE2.6, CYN.8, CMO.9, CMO.10 No protein-ligand interaction detected (PLIP) CYN.8: 13 residues within 4Å: Chain A: P.82, A.83, A.267, T.268, I.269, F.270, G.271 Ligands: PDT.4, FE2.5, FE2.6, CYN.7, CMO.9, CMO.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.82, A:A.83, A:I.269, A:F.270

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

CMO.9: 11 residues within 4Å: Chain A: A.81, P.82, A.83, T.119, P.177 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: A.83, A.267, T.268, I.269, F.270, G.271 Ligands: PDT.4, FE2.5, FE2.6, CYN.7, CYN.8, CMO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.269

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 4 residues within 4Å: Chain B: H.47, K.48, H.50, D.51 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.47, B:H.47, B:H.50, B:D.51

1 x HEC: HEME C(Covalent)

HEC.12: 24 residues within 4Å: Chain A: C.12, G.29 Chain C: Y.6, C.9, C.12, H.13, A.21, M.22, G.23, A.25, K.26, Q.31, L.36, M.40, Y.43, Y.48, G.50, E.51, R.52, M.55, M.56, N.58, A.59, Y.63 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:Y.6, C:M.22, C:A.25, C:L.36, C:A.59, C:Y.63 Hydrogen bonds: C:K.26, C:Q.31, C:Y.43, C:Y.48, C:E.51, C:R.52 Salt bridges: C:K.26 Metal complexes: C:H.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morelli, X. et al., Structural Model of the Fe-Hydrogenase/Cytochrome C553 Complex Combining Transverse Relaxation-Optimized Spectroscopy Experiments and Soft Docking Calculations. J.Biol.Chem. (2000)

Release Date

2000-08-25

Peptides

[FE]-HYDROGENASE (LARGE SUBUNIT): A
[FE]-HYDROGENASE (SMALL SUBUNIT): B
CYTOCHROME C553: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
E

[FE]-HYDROGENASE (LARGE SUBUNIT)

[FE]-HYDROGENASE (SMALL SUBUNIT)

CYTOCHROME C553

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