SMTL ID : 1j0o.1

High Resolution Crystal Structure of the wild type Tetraheme Cytochrome c3 from Desulfovibrio vulgaris Miyazaki F

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

monomer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 27 residues within 4Å: Chain A: M.11, D.12, K.13, T.14, Q.16, P.17, V.18, M.55, K.57, Y.65, Y.66, M.69, H.70, C.79, V.80, H.83, L.97, T.98, G.99, C.100, C.105, H.106 Ligands: HEM.4, EOH.5, EOH.7, EOH.10, EOH.12 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:T.14, A:Q.16, A:V.18, A:V.18, A:Y.65, A:Y.66, A:V.80 Hydrogen bonds: A:K.13, A:T.14, A:Q.16 Water bridges: A:K.15, A:K.15, A:M.55 pi-Stacking: A:Y.66 Metal complexes: A:H.70, A:H.106 HEM.2: 17 residues within 4Å: Chain A: C.33, H.34, H.35, V.37, D.42, Q.44, K.45, C.46, C.51, H.52, A.62, H.67, A.68, M.69, T.74, K.75, F.76 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:V.37, A:Q.44, A:F.76 Hydrogen bonds: A:K.75 Water bridges: A:K.75 Salt bridges: A:H.67, A:K.75 pi-Stacking: A:F.76 Metal complexes: A:H.35, A:H.52 HEM.3: 19 residues within 4Å: Chain A: P.2, K.3, A.4, P.5, L.9, M.11, F.20, H.22, H.25, V.28, K.29, C.30, C.33, H.34, Y.43, K.45, C.46 Ligands: HEM.4, EOH.8 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:P.2, A:P.5, A:L.9, A:L.9, A:F.20, A:F.20, A:F.20, A:V.28, A:Y.43, A:Y.43 Hydrogen bonds: A:C.46 Water bridges: A:Y.43, A:K.45, A:K.45 Salt bridges: A:K.45 Metal complexes: A:H.22, A:H.34 HEM.4: 17 residues within 4Å: Chain A: M.11, V.18, F.20, N.21, T.24, H.25, V.28, K.77, S.78, C.79, C.82, H.83, K.93, L.97, K.104 Ligands: HEM.1, HEM.3 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:V.18, A:F.20, A:T.24, A:V.28, A:L.97, A:K.104, A:K.104 Hydrogen bonds: A:N.21, A:T.24 Water bridges: A:K.93, A:K.93 Salt bridges: A:K.93 Metal complexes: A:H.25, A:H.83

8 x EOH: ETHANOL(Non-functional Binders)

EOH.5: 5 residues within 4Å: Chain A: Q.16, C.100, K.101, H.106 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) EOH.6: 2 residues within 4Å: Chain A: P.5, A.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.5, A:A.6 EOH.7: 3 residues within 4Å: Chain A: T.98, C.100 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:C.100 EOH.8: 7 residues within 4Å: Chain A: M.11, K.13, K.45, C.46, A.47, Y.65 Ligands: HEM.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.45, A:A.47 Hydrogen bonds: A:D.12, A:Y.65, A:Y.65 EOH.9: 2 residues within 4Å: Chain A: H.106, S.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.107 EOH.10: 3 residues within 4Å: Chain A: K.57, Y.66 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.66 EOH.11: 3 residues within 4Å: Chain A: A.47, D.53, M.55 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.53 EOH.12: 2 residues within 4Å: Chain A: C.100 Ligands: HEM.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ozawa, K. et al., Role of the aromatic ring of Tyr43 in tetraheme cytochrome c(3) from Desulfovibrio vulgaris Miyazaki F. Biophys.J. (2003)

Release Date

2003-11-19

Peptides

Cytochrome c3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytochrome c3

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