SMTL ID : 3ov0.1 (1 other biounit)

Structure of dodecaheme cytochrome c GSU1996

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

monomer

Ligands

12 x HEC: HEME C(Covalent)

HEC.1: 14 residues within 4Å: Chain A: K.4, V.6, F.8, F.18, H.20, H.23, L.24, N.30, C.31, C.34, H.35, L.41, P.44 Ligands: HEC.2 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:V.6, A:V.6, A:F.18, A:F.18, A:F.18, A:H.23, A:L.24, A:L.41, A:L.41 pi-Stacking: A:H.20 Metal complexes: A:H.20, A:H.35 HEC.2: 15 residues within 4Å: Chain A: V.16, F.18, I.22, H.23, Y.27, F.39, S.57, C.58, C.61, H.62, A.67, R.78, C.79 Ligands: HEC.1, HEC.3 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:V.16, A:F.18, A:I.22, A:Y.27, A:Y.27, A:F.39, A:A.67 pi-Stacking: A:F.18, A:H.23, A:H.62, A:F.68 Metal complexes: A:H.23, A:H.62 HEC.3: 18 residues within 4Å: Chain A: F.8, V.16, K.45, R.46, Y.47, T.48, M.49, F.68, V.70, Q.75, C.76, C.79, H.80, C.112, R.113, H.116 Ligands: HEC.2, HEC.4 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:F.8, A:F.8, A:V.16, A:F.68, A:R.113 Hydrogen bonds: A:Y.47, A:T.48, A:M.49 Metal complexes: A:H.80 HEC.4: 14 residues within 4Å: Chain A: L.10, K.11, N.12, H.80, F.99, H.101, H.104, V.105, G.110, C.112, C.115, H.116 Ligands: HEC.3, HEC.5 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:N.12, A:V.105 Hydrogen bonds: A:N.12 pi-Stacking: A:H.116 Metal complexes: A:H.101, A:H.116 HEC.5: 11 residues within 4Å: Chain A: V.98, F.99, H.104, I.121, C.138, C.141, H.142, M.146, A.147 Ligands: HEC.4, HEC.6 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:F.99, A:I.121, A:A.147 Hydrogen bonds: A:M.146 Metal complexes: A:H.104, A:H.142 HEC.6: 14 residues within 4Å: Chain A: Y.89, M.91, A.97, N.126, V.127, M.129, V.150, G.152, C.154, C.157, H.158, C.190, Y.200 Ligands: HEC.5 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:A.97, A:V.127, A:V.150 Hydrogen bonds: A:V.127, A:V.127, A:M.129 Metal complexes: A:H.158 HEC.7: 19 residues within 4Å: Chain A: M.161, P.163, P.164, V.167, F.169, F.179, H.181, H.184, L.185, Y.188, K.189, C.190, C.193, H.194, F.198, Y.200, K.201, A.202 Ligands: HEC.8 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:P.163, A:P.164, A:F.169, A:F.179, A:F.179, A:H.184, A:L.185, A:Y.188, A:F.198, A:F.198, A:Y.200, A:Y.200 Hydrogen bonds: A:Y.200 Metal complexes: A:H.194 HEC.8: 15 residues within 4Å: Chain A: F.169, F.179, H.184, M.187, Y.188, C.193, F.198, C.218, C.221, H.222, A.227, F.228, C.237 Ligands: HEC.7, HEC.9 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:F.169, A:F.179, A:F.179, A:Y.188, A:Y.188, A:F.198, A:F.198, A:A.227, A:F.228 Salt bridges: A:K.236 pi-Stacking: A:F.228 Metal complexes: A:H.184, A:H.222 HEC.9: 19 residues within 4Å: Chain A: F.169, V.174, A.177, R.206, F.207, T.208, M.209, A.210, C.218, H.222, F.228, S.230, A.231, C.234, C.237, H.238, L.241, Y.278 Ligands: HEC.8 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:F.169, A:V.174, A:V.174, A:A.177, A:H.222, A:F.228, A:L.241, A:Y.278 Hydrogen bonds: A:M.209, A:A.210 Salt bridges: A:R.206 Metal complexes: A:H.238 HEC.10: 18 residues within 4Å: Chain A: L.241, K.242, P.243, A.244, L.246, Y.248, F.257, H.259, H.262, L.263, F.266, C.268, C.271, H.272, F.276, Y.278, S.282 Ligands: HEC.11 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:L.241, A:P.243, A:L.246, A:L.246, A:F.257, A:F.257, A:H.262, A:L.263, A:F.266, A:F.276, A:F.276, A:Y.278 Hydrogen bonds: A:A.244, A:S.282 Salt bridges: A:H.259 pi-Stacking: A:Y.278 Metal complexes: A:H.259, A:H.272 HEC.11: 13 residues within 4Å: Chain A: Y.248, Y.256, F.257, H.262, F.266, F.276, C.296, C.299, H.300, D.304, A.305 Ligands: HEC.10, HEC.12 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:F.257, A:F.266, A:F.276, A:A.305 Metal complexes: A:H.262, A:H.300 HEC.12: 16 residues within 4Å: Chain A: Y.248, T.250, V.252, P.284, A.285, M.287, C.296, S.307, V.308, A.309, D.310, C.312, C.315, H.316, M.318 Ligands: HEC.11 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:Y.248, A:T.250, A:V.252, A:V.252 Hydrogen bonds: A:A.285, A:M.287 Metal complexes: A:H.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pokkuluri, P.R. et al., Structure of a novel dodecaheme cytochrome c from Geobacter sulfurreducens reveals an extended 12nm protein with interacting hemes. J.Struct.Biol. (2011)

Release Date

2010-12-29

Peptides

Cytochrome c family protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytochrome c family protein

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