SMTL ID : 6pw0.1 (1 other biounit)

Cytochrome C oxidase delta 6 mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 4 residues within 4Å: Chain B: P.96, F.99, N.100, E.103 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.103, B:E.103

1 x OH: HYDROXIDE ION(Non-covalent)

OH.2: 6 residues within 4Å: Chain A: G.283, H.284, V.287, H.334 Ligands: HEA.4, CU.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.334

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

HEA.3: 35 residues within 4Å: Chain A: G.38, T.48, M.51, R.52, W.95, I.99, H.102, M.106, M.107, V.110, V.111, A.114, G.171, W.172, Y.414, V.417, F.420, H.421, M.424, S.425, V.429, I.432, I.436, M.460, T.467, F.468, Q.471, R.481, R.482, Y.483, A.501, S.504, F.508, F.511 Ligands: DMU.5 30 PLIP interactions: 30 interactions with chain A, Hydrophobic interactions: A:T.48, A:I.99, A:M.106, A:V.111, A:A.114, A:V.417, A:F.420, A:F.420, A:V.429, A:I.432, A:I.436, A:T.467, A:F.468, A:A.501, A:F.508, A:F.508, A:F.511 Hydrogen bonds: A:T.48, A:R.52, A:W.172, A:Q.471, A:R.482, A:Y.483 Water bridges: A:R.481 Salt bridges: A:R.481, A:R.482 pi-Stacking: A:H.421, A:F.468 Metal complexes: A:H.102, A:H.421 HEA.4: 29 residues within 4Å: Chain A: W.172, W.280, V.287, Y.288, V.291, H.333, H.334, T.352, I.355, A.356, T.359, G.360, I.363, F.391, G.395, G.398, I.399, L.401, S.402, D.407, H.411, V.416, H.419, F.420, V.423, M.424, R.481 Chain B: I.43 Ligands: OH.2 31 PLIP interactions: 28 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:W.280, A:V.287, A:V.287, A:V.287, A:V.291, A:V.291, A:T.352, A:A.356, A:T.359, A:I.363, A:F.391, A:I.399, A:L.401, A:F.420, A:F.420, A:V.423, B:I.43, B:I.43 Hydrogen bonds: A:W.172, A:Y.288 Water bridges: A:H.334, A:D.412, A:R.481, A:R.481, A:R.481 Salt bridges: A:H.411, A:R.481, A:R.482 pi-Cation interactions: A:H.284 Metal complexes: A:H.419, H2O.1

6 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.5: 8 residues within 4Å: Chain A: V.31, L.34, F.35, I.436, M.443, S.444, P.545 Ligands: HEA.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.34, A:F.35, A:F.35, A:I.436, A:M.443 Water bridges: A:M.443 DMU.6: 11 residues within 4Å: Chain A: M.53, M.56, A.57, Q.61, F.62, S.83, A.84, V.85, F.502 Ligands: TRD.10, TRD.11 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.502, A:F.502 Hydrogen bonds: A:Q.61, A:Q.61, A:S.83 Water bridges: A:A.57, A:V.85 DMU.7: 6 residues within 4Å: Chain A: W.451, G.513, F.516, Y.517 Ligands: DMU.8, DMU.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.516, A:F.516 DMU.8: 7 residues within 4Å: Chain A: W.451, L.455, A.506, F.510 Ligands: DMU.7, DMU.9, TRD.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.455 DMU.9: 9 residues within 4Å: Chain A: P.449, W.451, L.509, F.510, G.513, V.514, Y.517 Ligands: DMU.7, DMU.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.449, A:W.451, A:F.510, A:F.510, A:V.514, A:Y.517 DMU.21: 7 residues within 4Å: Chain A: W.371 Chain B: L.50, F.69, H.71, N.72, L.75, W.79 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.50, B:L.75, B:W.79, A:W.371, A:W.371 Hydrogen bonds: B:N.72

10 x TRD: TRIDECANE(Non-covalent)

TRD.10: 4 residues within 4Å: Chain A: L.80, W.81, P.82 Ligands: DMU.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.81, A:P.82 TRD.11: 4 residues within 4Å: Chain A: F.495, L.499, F.502 Ligands: DMU.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.495, A:F.502, A:F.502 TRD.12: 5 residues within 4Å: Chain A: L.377, L.385, K.454, W.458 Ligands: TRD.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.377, A:L.385, A:L.385, A:W.458 TRD.13: 5 residues within 4Å: Chain A: W.451, K.454, W.458 Ligands: DMU.8, TRD.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.454, A:K.454, A:W.458 TRD.14: 1 residues within 4Å: Chain A: W.493 No protein-ligand interaction detected (PLIP) TRD.15: 6 residues within 4Å: Chain A: G.248, T.251, M.252, T.255, F.263, I.278 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.251, A:T.255, A:F.263, A:I.278 TRD.16: 7 residues within 4Å: Chain A: A.46, F.47, Y.50, F.76, S.79, L.94, M.98 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.46, A:F.47, A:Y.50, A:Y.50, A:F.76, A:F.76, A:L.94 TRD.22: 5 residues within 4Å: Chain B: T.27, H.30, W.31, G.34, F.35 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.27, B:W.31, B:W.31 TRD.23: 8 residues within 4Å: Chain B: F.131, T.171, A.172, V.174, K.243, V.245, W.253, H.257 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.131, B:F.131, B:A.172, B:V.245, B:W.253 TRD.24: 6 residues within 4Å: Chain A: F.469, F.473, R.476 Chain B: T.16, G.17, L.37 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.37, A:F.469, A:F.473

2 x HTH: (2S,3R)-heptane-1,2,3-triol(Non-covalent)

HTH.17: 6 residues within 4Å: Chain A: M.350, M.353 Chain B: L.87, V.88, G.91, A.92 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.87 Hydrogen bonds: B:L.87, B:G.91 HTH.25: 5 residues within 4Å: Chain B: E.127, E.128, A.251, E.255, H.258 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.127, B:E.128

3 x CU: COPPER (II) ION(Non-covalent)

CU.18: 4 residues within 4Å: Chain A: H.284, H.333, H.334 Ligands: OH.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.284, A:H.333, A:H.334, H2O.1 CU.26: 5 residues within 4Å: Chain B: C.227, E.229, C.231, H.235 Ligands: CU.27 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.227, B:E.229, B:C.231, B:H.235 CU.27: 5 residues within 4Å: Chain B: H.192, C.227, C.231, M.238 Ligands: CU.26 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.192, B:C.227, B:C.231

1 x MG: MAGNESIUM ION(Non-covalent)

MG.19: 4 residues within 4Å: Chain A: H.411, D.412 Chain B: S.228, E.229 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.411, B:E.229, H2O.1, H2O.1, H2O.8

1 x CA: CALCIUM ION(Non-covalent)

CA.20: 4 residues within 4Å: Chain A: E.54, A.57, G.59, Q.61 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.54, A:E.54, A:A.57, A:G.59, H2O.4

2 x CD: CADMIUM ION(Non-covalent)

CD.28: 3 residues within 4Å: Chain B: E.255, H.258, H.260 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.255, B:E.255, B:H.258, B:H.260 CD.29: 2 residues within 4Å: Chain B: H.71, E.76 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.71, B:E.76, B:E.76, H2O.9, H2O.11

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.30: 3 residues within 4Å: Chain B: S.130, F.131, E.132 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.130, B:E.132 Water bridges: B:E.132, B:E.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berg, J. et al., Structural changes at the surface of cytochrome c oxidase alter the proton-pumping stoichiometry. Biochim Biophys Acta Bioenerg (2019)

Release Date

2019-11-27

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

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

Cytochrome c oxidase subunit 2

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