SMTL ID : 3hb3.1

High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

2 x HEA: HEME-A(Non-covalent)

HEA.1: 33 residues within 4Å: Chain A: L.36, A.39, G.40, T.50, M.53, R.54, W.87, I.91, H.94, G.95, M.98, M.99, V.102, V.103, G.163, W.164, Y.406, F.412, H.413, M.416, S.417, V.421, I.424, F.425, M.452, I.459, F.460, Q.463, R.473, R.474, Y.475, S.496, F.500 29 PLIP interactions: 29 interactions with chain A, Hydrophobic interactions: A:T.50, A:I.91, A:M.98, A:V.103, A:F.412, A:V.421, A:I.424, A:F.425, A:I.459, A:F.500, A:F.500, A:F.500 Hydrogen bonds: A:R.54, A:W.87, A:W.164, A:Y.406, A:Q.463, A:R.474, A:Y.475 Water bridges: A:R.473, A:R.474 Salt bridges: A:R.473, A:R.474 pi-Stacking: A:F.412, A:H.413, A:H.413, A:F.460 Metal complexes: A:H.94, A:H.413 HEA.2: 33 residues within 4Å: Chain A: W.164, W.272, V.279, Y.280, I.282, I.283, H.325, H.326, T.344, I.347, A.348, T.351, G.352, F.356, F.383, T.384, G.387, V.388, G.390, L.393, S.394, D.399, H.403, V.408, H.411, F.412, V.415, M.416, R.473 Chain B: V.74, P.114, I.117 Ligands: PEO.18 34 PLIP interactions: 30 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:W.272, A:V.279, A:V.279, A:I.282, A:I.283, A:T.344, A:I.347, A:A.348, A:T.351, A:F.356, A:F.383, A:T.384, A:L.393, A:L.393, A:V.408, A:F.412, A:F.412, A:V.415, A:V.415, B:V.74, B:V.74, B:P.114, B:I.117 Hydrogen bonds: A:D.399 Water bridges: A:W.272, A:H.326, A:D.404, A:D.404, A:R.474 Salt bridges: A:H.403, A:R.473 pi-Stacking: A:H.325 pi-Cation interactions: A:H.276 Metal complexes: A:H.411

3 x CU1: COPPER (I) ION(Non-covalent)

CU1.3: 4 residues within 4Å: Chain A: H.276, H.325, H.326 Ligands: PEO.18 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.276, A:H.325, A:H.326 CU1.19: 5 residues within 4Å: Chain B: C.245, E.247, C.249, H.253 Ligands: CU1.20 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.245, B:E.247, B:C.249, B:H.253 CU1.20: 6 residues within 4Å: Chain B: H.210, C.245, E.247, C.249, M.256 Ligands: CU1.19 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.210, B:C.245, B:C.249

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 5 residues within 4Å: Chain A: H.403, D.404 Chain B: D.222, S.246, E.247 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.403, A:D.404, B:E.247, H2O.7, H2O.12

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: E.56, H.59, G.61, Q.63 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.56, A:E.56, A:H.59, A:G.61, H2O.4

10 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)(Non-functional Binders)

LDA.6: 6 residues within 4Å: Chain A: N.457, L.458, F.461, Y.484 Ligands: LMT.14, LMT.28 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.458, A:F.461 LDA.7: 5 residues within 4Å: Chain A: M.55, L.72, I.73 Ligands: LDA.9, LMT.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.72, A:I.73 LDA.8: 1 residues within 4Å: Chain A: Q.336 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:R.227, A:Q.336 Hydrogen bonds: A:Q.336 LDA.9: 5 residues within 4Å: Chain A: Y.52, A.70, R.71, L.72 Ligands: LDA.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.52, A:L.72, A:L.72 LDA.21: 7 residues within 4Å: Chain A: T.389, Y.407, F.461, H.464, R.468 Chain B: N.48 Ligands: LDA.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.461, A:H.464 LDA.22: 4 residues within 4Å: Chain B: H.65, F.66 Ligands: LDA.25, LMT.29 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.66 LDA.23: 4 residues within 4Å: Chain A: F.461 Chain B: Y.69 Ligands: LDA.21, LDA.26 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.69, A:F.461 LDA.24: 3 residues within 4Å: Chain B: R.131 Ligands: LMT.27, LMT.29 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.131 LDA.25: 4 residues within 4Å: Chain B: H.65, Y.69, A.73 Ligands: LDA.22 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.69, B:A.73 LDA.26: 1 residues within 4Å: Ligands: LDA.23 No protein-ligand interaction detected (PLIP)

14 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.10: 5 residues within 4Å: Chain A: W.443, L.447, A.498, F.502 Ligands: LMT.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.443, A:L.447, A:F.502 LMT.11: 5 residues within 4Å: Chain A: P.441, W.443, G.505, Y.509 Ligands: LMT.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.443 LMT.12: 10 residues within 4Å: Chain A: R.21, I.33, L.36, F.37, M.435, S.436, I.504, L.511, P.537 Ligands: LMT.17 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.37, A:I.504, A:L.511 Hydrogen bonds: A:R.21, A:R.21 LMT.13: 10 residues within 4Å: Chain A: V.51, M.55, Q.58, Y.64, A.74, A.76, Y.494, F.497, L.501 Ligands: LDA.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.51, A:Y.494, A:F.497, A:L.501 Hydrogen bonds: A:Y.64, A:Y.64, A:A.74 Water bridges: A:H.59, A:Y.494 LMT.14: 5 residues within 4Å: Chain A: Y.484, N.487, I.488, I.491 Ligands: LDA.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.484, A:N.487 LMT.15: 9 residues within 4Å: Chain A: F.369, L.374, F.377, G.378, F.381, W.450, F.453 Chain B: I.86, R.92 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.369, A:L.374, A:F.381, A:W.450, A:F.453, B:I.86 LMT.16: 3 residues within 4Å: Chain A: R.129, L.130, L.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.129 Salt bridges: A:R.129 LMT.17: 8 residues within 4Å: Chain A: W.22, F.23, L.34, F.37, R.438, L.511, F.512 Ligands: LMT.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.22, A:F.23, A:F.37, A:F.512 Hydrogen bonds: A:R.438 LMT.27: 6 residues within 4Å: Chain B: L.126, P.127, F.130, R.131, E.134 Ligands: LDA.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.131, B:E.134, B:E.134 LMT.28: 7 residues within 4Å: Chain A: F.461, Y.484, W.485 Chain B: N.44, G.45, M.47 Ligands: LDA.6 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.44, B:G.45, A:Y.484 Water bridges: B:N.44, B:G.45 Hydrophobic interactions: A:F.461, A:F.461, A:F.461 LMT.29: 8 residues within 4Å: Chain B: W.62, L.116, F.124, I.128, R.131 Chain D: N.28 Ligands: LDA.22, LDA.24 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain B Water bridges: D:N.28, D:N.28 Hydrophobic interactions: B:L.116, B:F.124, B:F.124 Hydrogen bonds: B:R.131, B:R.131 LMT.30: 7 residues within 4Å: Chain A: W.363 Chain B: L.81, F.100, H.102, N.103, W.110 Ligands: LMT.32 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.81, B:F.100, B:F.100, B:W.110, B:W.110 Hydrogen bonds: B:N.103 Water bridges: B:H.102 LMT.31: 6 residues within 4Å: Chain A: L.342, M.345, T.346, V.349 Chain B: V.115, L.118 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.342, A:M.345, A:T.346, A:V.349, B:V.115, B:L.118, B:L.118 LMT.32: 6 residues within 4Å: Chain A: F.356 Chain B: F.77, I.109, V.113, P.114 Ligands: LMT.30 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.356, B:F.77, B:F.77, B:F.77, B:F.77, B:I.109

1 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.18: 7 residues within 4Å: Chain A: H.276, V.279, H.325, H.326, H.411 Ligands: HEA.2, CU1.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koepke, J. et al., High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: New insights into the active site and the proton transfer pathways. Biochim.Biophys.Acta (2009)

Release Date

2009-06-23

Peptides

Cytochrome c oxidase subunit 1-beta: A
Cytochrome c oxidase subunit 2: B
ANTIBODY FV FRAGMENT: C
ANTIBODY FV FRAGMENT: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c oxidase subunit 1-beta

Cytochrome c oxidase subunit 2

ANTIBODY FV FRAGMENT

ANTIBODY FV FRAGMENT

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