SMTL ID : 1sp3.1

Crystal structure of octaheme cytochrome c from Shewanella oneidensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.1: 5 residues within 4Å: Chain A: N.61, F.63, C.64, K.153 Ligands: HEC.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.61, A:C.64

8 x HEC: HEME C(Covalent)(Non-covalent)

HEC.2: 17 residues within 4Å: Chain A: N.2, P.3, H.4, L.8, V.18, Q.21, C.22, T.24, C.25, H.26, C.98, H.102, A.128, V.131, G.132, A.133 Ligands: HEC.4 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:N.2, A:P.3, A:L.8, A:V.18, A:A.128 Hydrogen bonds: A:A.133 Metal complexes: A:H.4, A:H.26 HEC.3: 22 residues within 4Å: Chain A: K.56, S.59, N.61, C.64, V.65, A.66, I.67, R.73, C.74, S.76, C.77, C.142, H.143, Y.145, G.146, K.153, H.154, M.394, W.396 Ligands: SCN.1, HEC.5, HEC.6 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:K.56, A:K.56, A:I.67, A:Y.145 Hydrogen bonds: A:N.61 Water bridges: A:M.197, A:W.396 Salt bridges: A:K.153, A:H.154 HEC.4: 15 residues within 4Å: Chain A: H.26, Q.29, H.38, A.79, V.96, D.97, C.98, C.101, H.102, P.134, Q.182, T.187, H.190 Ligands: HEC.2, HEC.5 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:H.26, A:Q.29, A:A.79, A:V.96, A:P.134, A:T.187 Hydrogen bonds: A:Q.29, A:Q.182 Water bridges: A:K.189, A:H.190 Salt bridges: A:H.190 Metal complexes: A:H.102, A:H.190 HEC.5: 24 residues within 4Å: Chain A: S.37, H.38, W.41, E.42, L.43, G.55, K.56, C.77, H.78, A.79, I.100, C.101, N.138, C.139, C.142, H.143, C.181, H.185, I.192, S.193, G.194 Ligands: HEC.3, HEC.4, HEC.6 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:W.41, A:K.56, A:I.100 Hydrogen bonds: A:S.37, A:K.56 Water bridges: A:Q.191, A:Q.191 Metal complexes: A:H.38, A:H.143 HEC.6: 24 residues within 4Å: Chain A: C.139, H.143, F.144, H.154, L.157, H.171, M.172, C.181, C.184, H.185, G.194, N.195, A.196, M.197, D.205, H.206, I.207, G.208, R.397, N.399, H.400 Ligands: HEC.3, HEC.5, HEC.7 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:H.143, A:F.144, A:L.157, A:H.171, A:N.399 Hydrogen bonds: A:N.195, A:M.197, A:H.206, A:I.207 Water bridges: A:R.397, A:N.399 Salt bridges: A:H.154 Metal complexes: A:H.185, A:H.400 HEC.7: 19 residues within 4Å: Chain A: V.170, H.171, N.177, F.179, C.184, I.207, G.208, C.209, C.212, H.213, C.232, Q.233, H.236, N.399, V.402, P.404, K.405 Ligands: HEC.6, HEC.8 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:V.170, A:F.179, A:F.179, A:I.207, A:Q.233, A:H.236, A:V.402, A:V.402 Hydrogen bonds: A:K.405 Water bridges: A:K.166, A:N.177, A:K.405 Salt bridges: A:K.166, A:K.405 Metal complexes: A:H.171, A:H.213 HEC.8: 19 residues within 4Å: Chain A: C.209, H.213, S.215, P.217, H.218, L.223, H.226, T.227, V.230, A.231, C.232, C.235, H.236, K.405, A.408, L.409, N.410 Ligands: HEC.7, HEC.9 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:H.213, A:L.223, A:L.223, A:H.226, A:T.227, A:V.230, A:K.405, A:A.408 Water bridges: A:P.217, A:S.219 Salt bridges: A:K.405 Metal complexes: A:H.218, A:H.236 HEC.9: 22 residues within 4Å: Chain A: N.220, K.222, L.223, H.226, T.229, V.230, T.234, C.235, I.326, L.409, N.410, C.411, C.414, H.415, L.421, W.423, Y.428, P.432, M.433, K.440, H.441 Ligands: HEC.8 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:K.222, A:L.223, A:T.229, A:V.230, A:T.234, A:I.326, A:L.409, A:W.423, A:Y.428, A:P.432, A:P.432 Hydrogen bonds: A:T.229, A:H.441 Water bridges: A:T.225, A:H.226 Salt bridges: A:K.222 Metal complexes: A:H.226, A:H.415

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mowat, C.G. et al., Octaheme tetrathionate reductase is a respiratory enzyme with novel heme ligation. Nat.Struct.Mol.Biol. (2004)

Release Date

2004-09-21

Peptides

cytochrome c, putative: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

cytochrome c, putative