SMTL ID : 1czj.1

CYTOCHROME C OF CLASS III (AMBLER) 26 KD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-dimer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: R.91, R.95 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.91, A:R.95 SO4.6: 2 residues within 4Å: Chain B: R.91, R.95 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.91, B:R.95

8 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.2: 21 residues within 4Å: Chain A: F.3, I.5, P.6, V.9, M.11, F.28, H.30, H.33, M.34, I.36, A.37, C.38, C.41, H.42, I.51, S.53, C.54 Chain B: T.2, Q.39, V.45 Ligands: HEM.4 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.3, A:F.3, A:F.3, A:I.5, A:P.6, A:V.9, A:F.28, A:F.28, A:F.28, A:H.33, A:I.36, A:I.51, A:I.51, B:V.45 Hydrogen bonds: A:I.51, A:S.53, A:C.54, A:M.55 Metal complexes: A:H.30, A:H.42 HEM.3: 15 residues within 4Å: Chain A: C.41, H.42, H.43, T.44, E.52, S.53, C.54, T.56, C.59, H.60, I.69, R.74, T.75, F.76, K.84 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:T.44, A:E.52, A:I.69, A:T.75, A:F.76 Hydrogen bonds: A:D.81, A:D.81 Salt bridges: A:H.43, A:R.74 pi-Cation interactions: A:K.84 Metal complexes: A:H.43, A:H.60 HEM.4: 17 residues within 4Å: Chain A: V.26, F.28, N.29, S.32, H.33, I.36, Q.40, E.83, K.84, S.85, C.86, C.89, H.90, L.93, D.100, P.102 Ligands: HEM.2 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:V.26, A:I.36, A:L.93, A:P.102 Hydrogen bonds: A:N.29, A:S.32, A:D.100, A:A.101 Water bridges: A:N.29 pi-Stacking: A:F.28 Metal complexes: A:H.33, A:H.90 HEM.5: 21 residues within 4Å: Chain A: M.11, S.12, P.13, Y.19, P.21, K.22, K.23, V.26, V.72, Y.73, F.76, H.77, C.86, V.87, H.90, P.102, L.103, A.104, C.105, C.108, H.109 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:M.11, A:P.13, A:V.72, A:Y.73, A:Y.73, A:F.76, A:F.76, A:F.76, A:V.87 Hydrogen bonds: A:Y.19, A:Y.19, A:K.22, A:K.23, A:V.26 Salt bridges: A:H.109 pi-Stacking: A:Y.73 Metal complexes: A:H.77, A:H.109 HEM.7: 21 residues within 4Å: Chain A: T.2, Q.39, V.45 Chain B: F.3, I.5, P.6, V.9, M.11, F.28, H.30, H.33, M.34, I.36, A.37, C.38, C.41, H.42, I.51, S.53, C.54 Ligands: HEM.9 22 PLIP interactions: 19 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:F.3, B:F.3, B:F.3, B:I.5, B:P.6, B:V.9, B:F.28, B:F.28, B:F.28, B:H.33, B:I.36, B:I.51, B:I.51, A:V.45 Hydrogen bonds: B:I.51, B:S.53, B:C.54, B:M.55, A:T.2, A:T.2 Metal complexes: B:H.30, B:H.42 HEM.8: 15 residues within 4Å: Chain B: C.41, H.42, H.43, T.44, E.52, S.53, C.54, T.56, C.59, H.60, I.69, R.74, T.75, F.76, K.84 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:T.44, B:E.52, B:I.69, B:T.75, B:F.76 Hydrogen bonds: B:D.81 Salt bridges: B:H.43, B:R.74 pi-Cation interactions: B:K.84 Metal complexes: B:H.43, B:H.60 HEM.9: 17 residues within 4Å: Chain B: V.26, F.28, N.29, S.32, H.33, I.36, Q.40, E.83, K.84, S.85, C.86, C.89, H.90, L.93, D.100, P.102 Ligands: HEM.7 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:V.26, B:I.36, B:L.93, B:P.102 Hydrogen bonds: B:N.29, B:S.32, B:D.100, B:A.101 Water bridges: B:N.29 pi-Stacking: B:F.28 Metal complexes: B:H.33, B:H.90 HEM.10: 21 residues within 4Å: Chain B: M.11, S.12, P.13, Y.19, P.21, K.22, K.23, V.26, V.72, Y.73, F.76, H.77, C.86, V.87, H.90, P.102, L.103, A.104, C.105, C.108, H.109 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:M.11, B:P.13, B:V.72, B:Y.73, B:Y.73, B:F.76, B:F.76, B:F.76, B:V.87 Hydrogen bonds: B:Y.19, B:K.22, B:K.23, B:V.26 Salt bridges: B:H.109 pi-Stacking: B:Y.73 Metal complexes: B:H.77, B:H.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Czjzek, M. et al., Crystal structure of a dimeric octaheme cytochrome c3 (M(r) 26,000) from Desulfovibrio desulfuricans Norway. Structure (1996)

Release Date

1996-07-11

Peptides

CYTOCHROME C3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CYTOCHROME C3