SMTL ID : 3hq9.1

CcpA from G. sulfurreducens, S134P variant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-dimer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)(Non-covalent)

HEM.1: 24 residues within 4Å: Chain A: I.71, S.72, C.73, C.76, H.77, S.90, T.91, G.92, R.100, N.101, A.102, P.103, S.108, N.111, F.115, W.116, V.131, E.136, M.137, I.178, E.182 Ligands: IMD.4, OXL.6, BU3.8 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:I.71, A:P.103, A:V.131, A:V.131, A:E.136, A:E.136, A:I.178 Hydrogen bonds: A:N.111, A:W.116 Water bridges: A:Q.114, A:D.117, A:R.268, A:R.268, A:R.268 Salt bridges: A:R.268 Metal complexes: A:H.77 HEM.2: 22 residues within 4Å: Chain A: W.116, G.218, C.219, C.222, H.223, F.236, G.237, V.238, F.267, R.268, A.269, P.270, L.272, Y.281, F.282, H.283, V.294, M.297, F.302, I.304, L.306, I.314 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:F.236, A:F.267, A:A.269, A:P.270, A:L.272, A:L.272, A:F.282, A:F.282, A:V.294, A:M.297, A:F.302, A:F.302, A:F.302, A:I.304, A:L.306, A:I.314 Hydrogen bonds: A:V.238, A:F.282, A:H.283 Water bridges: A:T.278 Salt bridges: A:H.283 pi-Stacking: A:F.302 Metal complexes: A:H.223 HEM.9: 23 residues within 4Å: Chain B: I.71, S.72, C.73, C.76, H.77, S.90, T.91, R.100, N.101, A.102, P.103, S.108, N.111, A.113, Q.114, F.115, W.116, E.136, M.137, I.178, E.182, R.268 Ligands: IMD.12 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:I.71, B:P.103, B:P.103, B:E.136, B:I.178 Hydrogen bonds: B:N.111, B:Q.114, B:W.116 Water bridges: B:Q.114, B:D.117, B:R.268, B:R.268, B:R.268 Salt bridges: B:R.268 Metal complexes: B:H.77 HEM.10: 22 residues within 4Å: Chain B: W.116, G.218, C.219, C.222, H.223, F.234, F.236, G.237, V.238, F.267, R.268, A.269, P.270, L.272, Y.281, F.282, H.283, M.297, F.302, I.304, L.306, I.314 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:F.234, B:F.236, B:F.267, B:P.270, B:L.272, B:L.272, B:F.282, B:M.297, B:F.302, B:F.302, B:F.302, B:I.304, B:L.306, B:I.314 Hydrogen bonds: B:V.238, B:F.282, B:H.283 Water bridges: B:T.278 Salt bridges: B:H.283 pi-Stacking: B:F.302 Metal complexes: B:H.223

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: N.101, T.278, P.280 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.278, A:P.280, H2O.1, H2O.1, H2O.2 CA.11: 3 residues within 4Å: Chain B: N.101, T.278, P.280 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.278, B:P.280, H2O.11, H2O.12, H2O.14

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 6 residues within 4Å: Chain A: V.131, Q.132, A.133, E.136 Ligands: HEM.1, BU3.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.136 IMD.5: 10 residues within 4Å: Chain A: G.80, L.81, G.82, L.86, I.277, Y.279 Chain B: R.64, M.333, P.334, A.335 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:M.333 Hydrogen bonds: A:Y.279, A:Y.279 IMD.12: 2 residues within 4Å: Chain B: P.134 Ligands: HEM.9 No protein-ligand interaction detected (PLIP) IMD.13: 10 residues within 4Å: Chain A: R.64, M.333, P.334, A.335 Chain B: G.80, L.81, G.82, L.86, I.277, Y.279 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:M.333 Hydrogen bonds: B:Y.279, B:Y.279

4 x OXL: OXALATE ION(Non-covalent)

OXL.6: 9 residues within 4Å: Chain A: L.65, V.131, Q.132, A.133, N.139, V.144, F.171, M.174 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.65, A:L.65, A:A.133 OXL.7: 6 residues within 4Å: Chain A: S.336, T.337, D.338 Chain B: Y.279, W.288, S.289 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.288, B:W.288 Water bridges: B:L.290, A:R.342 OXL.14: 5 residues within 4Å: Chain A: Y.279, W.288, S.289 Chain B: S.336, T.337 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:W.288, B:S.336 Water bridges: A:L.290, B:D.338 OXL.15: 5 residues within 4Å: Chain A: T.75, W.95 Chain B: L.70, T.75, W.95 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.70

2 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.8: 6 residues within 4Å: Chain A: Q.114, F.115, V.131, Q.132 Ligands: HEM.1, IMD.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.115, A:F.115 Hydrogen bonds: A:Q.114, A:Q.132 BU3.16: 4 residues within 4Å: Chain B: Q.132, A.175, I.178, E.179 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.179 Hydrogen bonds: B:A.175, B:E.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hoffmann, M. et al., CcpA from Geobacter sulfurreducens is a basic di-heme cytochrome c peroxidase. J.Mol.Biol. (2009)

Release Date

2009-09-22

Peptides

Cytochrome c551 peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytochrome c551 peroxidase