- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 1 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)
- 11 x TRD: TRIDECANE(Non-covalent)
- 5 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)
DMU.12: 6 residues within 4Å:- Chain A: V.15, F.19, M.427, S.428, I.499, P.529
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:F.19, A:F.19, A:F.19, A:M.427, A:I.499
DMU.13: 7 residues within 4Å:- Chain A: P.433, W.435, F.494, G.497, V.498, Y.501
- Ligands: DMU.14
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:W.435, A:F.494, A:V.498, A:Y.501
- Water bridges: A:Y.501
DMU.14: 5 residues within 4Å:- Chain A: W.435, A.490, F.494
- Ligands: TRD.5, DMU.13
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:A.490, A:F.494
DMU.15: 11 residues within 4Å:- Chain A: V.33, M.40, Q.45, F.46, P.66, S.67, V.69, F.486, F.489
- Ligands: TRD.2, TRD.3
10 PLIP interactions:10 interactions with chain A- Hydrophobic interactions: A:V.33, A:F.486, A:F.486, A:F.486, A:F.489
- Hydrogen bonds: A:Q.45, A:Q.45, A:S.67
- Water bridges: A:V.69, A:V.69
DMU.23: 8 residues within 4Å:- Chain A: I.351, A.352, W.355
- Chain B: L.47, F.66, H.68, N.69, L.72
9 PLIP interactions:3 interactions with chain A, 6 interactions with chain B- Hydrophobic interactions: A:I.351, A:A.352, A:W.355, B:L.47, B:L.72
- Hydrogen bonds: B:H.68, B:N.69
- Water bridges: B:H.68, B:H.68
- 2 x HEA: HEME-A(Non-covalent)
HEA.16: 37 residues within 4Å:- Chain A: L.18, G.21, G.22, V.29, T.32, M.35, R.36, W.79, I.83, H.86, G.87, M.90, M.91, V.94, V.95, A.98, G.155, W.156, Y.398, V.401, F.404, H.405, M.408, S.409, V.413, I.416, M.444, T.451, F.452, Q.455, R.465, R.466, Y.467, A.485, S.488, F.492, F.495
31 PLIP interactions:31 interactions with chain A,- Hydrophobic interactions: A:V.29, A:T.32, A:I.83, A:M.90, A:V.95, A:A.98, A:V.401, A:F.404, A:F.404, A:M.408, A:V.413, A:I.416, A:T.451, A:F.452, A:A.485, A:F.492, A:F.492, A:F.495
- Hydrogen bonds: A:T.32, A:R.36, A:W.156, A:Q.455, A:R.466, A:Y.467
- Water bridges: A:R.465
- Salt bridges: A:R.465, A:R.466
- pi-Stacking: A:H.405, A:F.452
- Metal complexes: A:H.86, A:H.405
HEA.17: 29 residues within 4Å:- Chain A: M.91, W.156, W.264, V.271, Y.272, V.275, H.317, H.318, T.336, I.339, A.340, T.343, G.344, I.347, F.375, G.379, G.382, I.383, L.385, S.386, D.391, H.395, V.400, H.403, F.404, V.407, M.408, R.465
- Chain B: I.40
30 PLIP interactions:28 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions,- Hydrophobic interactions: A:W.264, A:V.271, A:V.271, A:V.271, A:V.275, A:T.336, A:A.340, A:T.343, A:I.347, A:F.375, A:I.383, A:L.385, A:F.404, A:F.404, A:V.407, B:I.40
- Hydrogen bonds: A:W.156, A:Y.272, A:Y.272
- Water bridges: A:T.343, A:D.396, A:D.396, A:R.465, A:R.465
- Salt bridges: A:H.395, A:R.465, A:R.466
- pi-Cation interactions: A:H.268
- Metal complexes: A:H.403, H2O.3
- 3 x CU: COPPER (II) ION(Non-covalent)
CU.18: 3 residues within 4Å:- Chain A: H.268, H.317, H.318
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:H.268, A:H.317, A:H.318, H2O.3, H2O.5
CU.25: 5 residues within 4Å:- Chain B: C.224, E.226, C.228, H.232
- Ligands: CU.26
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:C.224, B:E.226, B:C.228, B:H.232
CU.26: 5 residues within 4Å:- Chain B: H.189, C.224, C.228, M.235
- Ligands: CU.25
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:H.189, B:C.224, B:C.228
- 1 x MG: MAGNESIUM ION(Non-covalent)
- 1 x CA: CALCIUM ION(Non-covalent)
- 2 x HTH: (2S,3R)-heptane-1,2,3-triol(Non-covalent)
HTH.21: 8 residues within 4Å:- Chain A: M.334, M.337, V.338
- Chain B: L.84, V.85, G.88, A.89, L.92
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: B:L.84, B:L.84, B:V.85, A:V.338
HTH.29: 5 residues within 4Å:- Chain B: E.124, A.248, L.251, E.252, H.255
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:L.251
- Hydrogen bonds: B:E.124
- 1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 2 x CD: CADMIUM ION(Non-covalent)
CD.27: 3 residues within 4Å:- Chain B: E.252, H.255, H.257
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:E.252, B:E.252, B:H.255, B:H.257
CD.28: 2 residues within 4Å:- Chain B: H.68, E.73
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:H.68, B:E.73, B:E.73, H2O.7, H2O.11
- 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
AB
B - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 1 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)
- 11 x TRD: TRIDECANE(Non-covalent)
- 5 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)
- 2 x HEA: HEME-A(Non-covalent)
- 3 x CU: COPPER (II) ION(Non-covalent)
- 1 x MG: MAGNESIUM ION(Non-covalent)
- 1 x CA: CALCIUM ION(Non-covalent)
- 2 x HTH: (2S,3R)-heptane-1,2,3-triol(Non-covalent)
- 1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 2 x CD: CADMIUM ION(Non-covalent)
- 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
AB
B - Membrane
-
We predict this structure to be a membrane protein.