SMTL ID : 1wr5.1

Three dimensional Structure of the E41K mutant of Tetraheme Cytochrome c3 from Desulfovibrio vulgaris Miyazaki F

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 24 residues within 4Å: Chain A: M.12, D.13, K.14, T.15, Q.17, P.18, V.19, M.56, K.58, Y.66, Y.67, M.70, H.71, C.80, V.81, H.84, L.98, T.99, G.100, C.101, C.106, H.107 Ligands: EOH.5, EOH.11 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:T.15, A:Q.17, A:V.19, A:Y.66, A:Y.67, A:M.70, A:V.81 Hydrogen bonds: A:K.14, A:T.15, A:Q.17 Water bridges: A:K.16, A:K.16, A:M.56 pi-Stacking: A:Y.67 Metal complexes: A:H.71, A:H.107 HEC.2: 20 residues within 4Å: Chain A: C.34, H.35, H.36, V.38, D.43, Q.45, K.46, C.47, C.52, H.53, A.63, H.68, A.69, M.70, T.75, K.76, F.77, K.78 Ligands: EOH.8, EOH.14 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:V.38, A:Q.45, A:F.77 Hydrogen bonds: A:K.76 Salt bridges: A:H.68, A:K.76 pi-Stacking: A:F.77 Metal complexes: A:H.36, A:H.53 HEC.3: 19 residues within 4Å: Chain A: P.3, K.4, A.5, P.6, L.10, M.12, F.21, H.23, H.26, V.29, K.30, C.31, C.34, H.35, Y.44, K.46, C.47 Ligands: HEC.4, EOH.5 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:P.6, A:L.10, A:F.21, A:F.21, A:F.21, A:F.21, A:V.29, A:Y.44, A:Y.44 Hydrogen bonds: A:Y.44, A:C.47 Salt bridges: A:K.46 Metal complexes: A:H.23, A:H.35 HEC.4: 19 residues within 4Å: Chain A: M.12, V.19, F.21, N.22, T.25, H.26, V.29, K.78, S.79, C.80, C.83, H.84, K.94, L.98, K.105, C.106 Ligands: HEC.3, EOH.9, EOH.13 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:V.19, A:F.21, A:T.25, A:V.29, A:L.98, A:K.105 Hydrogen bonds: A:N.22, A:T.25 Water bridges: A:K.94, A:K.94 Salt bridges: A:K.94 Metal complexes: A:H.26, A:H.84

14 x EOH: ETHANOL(Non-functional Binders)

EOH.5: 10 residues within 4Å: Chain A: M.12, D.13, K.14, K.46, C.47, A.48, Y.66 Ligands: HEC.1, HEC.3, EOH.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.46, A:A.48 Hydrogen bonds: A:D.13, A:Y.66, A:Y.66 EOH.6: 3 residues within 4Å: Chain A: K.14, K.46 Ligands: EOH.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.46 Water bridges: A:T.49 EOH.7: 4 residues within 4Å: Chain A: K.73, L.85, E.86 Ligands: EOH.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.86 Hydrogen bonds: A:K.73 EOH.8: 2 residues within 4Å: Chain A: A.63 Ligands: HEC.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.63 EOH.9: 2 residues within 4Å: Chain A: A.28 Ligands: HEC.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.28 EOH.10: 1 residues within 4Å: Chain A: K.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.95 EOH.11: 3 residues within 4Å: Chain A: T.99, C.101 Ligands: HEC.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.99 Water bridges: A:T.99 EOH.12: 2 residues within 4Å: Chain A: K.102, S.108 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.17 EOH.13: 3 residues within 4Å: Chain A: A.28, V.29 Ligands: HEC.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.29 EOH.14: 4 residues within 4Å: Chain A: V.38, N.39, D.43 Ligands: HEC.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.38 EOH.15: 3 residues within 4Å: Chain A: Y.67, H.71, D.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.67, A:Y.67 EOH.16: 1 residues within 4Å: Chain A: K.46 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.46 EOH.17: 1 residues within 4Å: Chain A: K.105 No protein-ligand interaction detected (PLIP) EOH.18: 3 residues within 4Å: Chain A: E.86, G.89 Ligands: EOH.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.86

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

2004-10-26

Peptides

Cytochrome c3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytochrome c3