- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.32 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 2 x HEA: HEME-A(Non-covalent)
- 3 x CU: COPPER (II) ION(Non-covalent)
CU.3: 4 residues within 4Å:- Chain A: H.276, H.325, H.326
- Ligands: PER.18
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:H.276, A:H.325, A:H.326
CU.19: 5 residues within 4Å:- Chain B: C.245, E.247, C.249, H.253
- Ligands: CU.20
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:C.245, B:E.247, B:C.249, B:H.253
CU.20: 5 residues within 4Å:- Chain B: H.210, C.245, C.249, M.256
- Ligands: CU.19
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:H.210, B:C.245, B:C.249
- 1 x MG: MAGNESIUM ION(Non-covalent)
- 1 x CA: CALCIUM ION(Non-covalent)
- 9 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
LDA.6: 6 residues within 4Å:- Chain A: L.458, Y.484, W.485, I.488
- Ligands: LMT.14, LMT.27
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:L.458, A:W.485
LDA.7: 5 residues within 4Å:- Chain A: C.48, V.51, M.55, L.72
- Ligands: LMT.13
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:V.51, A:L.72
LDA.8: 2 residues within 4Å:- Chain A: H.269, Q.336
No protein-ligand interaction detected (PLIP)LDA.9: 6 residues within 4Å:- Chain A: W.22, L.34, F.37, L.511, F.512
- Ligands: LMT.12
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:W.22, A:W.22, A:L.34, A:F.37, A:F.512
LDA.21: 5 residues within 4Å:- Chain A: F.465, R.468
- Chain B: N.48, L.68
- Ligands: LDA.24
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: B:L.68, A:F.465
LDA.22: 7 residues within 4Å:- Chain B: H.65, F.66, Y.69, I.70, L.116, I.117, A.120
8 PLIP interactions:8 interactions with chain B- Hydrophobic interactions: B:F.66, B:F.66, B:Y.69, B:Y.69, B:I.70, B:L.116, B:I.117, B:A.120
LDA.23: 7 residues within 4Å:- Chain A: F.356
- Chain B: F.77, I.106, I.109, W.110, V.113
- Ligands: LMT.28
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: B:F.77, B:F.77, B:V.113, A:F.356
LDA.24: 7 residues within 4Å:- Chain B: H.65, L.68, Y.69, T.72, T.75
- Ligands: LDA.21, LMT.27
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:L.68, B:Y.69
- Water bridges: B:H.65
LDA.25: 3 residues within 4Å:- Chain B: A.123
- Ligands: LMT.26, LMT.29
1 PLIP interactions:1 interactions with chain B- pi-Cation interactions: B:F.124
- 12 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
LMT.10: 4 residues within 4Å:- Chain A: W.443, L.447, F.502
- Ligands: LMT.11
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:W.443, A:L.447, A:F.502, A:F.502, A:F.502
LMT.11: 7 residues within 4Å:- Chain A: P.441, W.443, L.501, G.505, I.506, Y.509
- Ligands: LMT.10
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:W.443
- Hydrogen bonds: A:W.443, A:Y.509
LMT.12: 11 residues within 4Å:- Chain A: R.21, W.22, L.36, F.37, G.40, M.435, S.436, I.504, L.511, P.537
- Ligands: LDA.9
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:L.36, A:F.37, A:F.37, A:I.504, A:L.511
- Hydrogen bonds: A:R.21
LMT.13: 7 residues within 4Å:- Chain A: Q.58, H.59, Y.64, A.74, Y.494, F.497
- Ligands: LDA.7
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:F.497
- Hydrogen bonds: A:Y.64, A:Y.64
- Water bridges: A:A.74
LMT.14: 7 residues within 4Å:- Chain A: M.451, I.454, N.487, I.491, Y.494, A.498
- Ligands: LDA.6
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:I.454, A:A.498
- Hydrogen bonds: A:N.487
LMT.15: 7 residues within 4Å:- Chain A: F.369, L.374, F.377, F.381, F.453
- Chain B: L.82, I.86
7 PLIP interactions:5 interactions with chain A, 2 interactions with chain B- Hydrophobic interactions: A:F.369, A:L.374, A:F.377, A:F.381, A:F.453, B:L.82, B:I.86
LMT.16: 10 residues within 4Å:- Chain A: L.342, M.345, T.346, V.349
- Chain B: V.115, L.118, V.119, G.122, A.123, L.126
5 PLIP interactions:3 interactions with chain B, 2 interactions with chain A- Hydrophobic interactions: B:V.115, B:L.118, B:L.126, A:L.342, A:V.349
LMT.17: 6 residues within 4Å:- Chain A: M.24, T.26, R.129, L.130, N.132, L.133
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:L.130, A:L.133, A:L.133
- Hydrogen bonds: A:M.24
LMT.26: 6 residues within 4Å:- Chain B: L.126, P.127, F.130, R.131, E.134
- Ligands: LDA.25
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:R.131, B:R.131, B:E.134
LMT.27: 8 residues within 4Å:- Chain A: F.461, Y.484, W.485
- Chain B: N.44, G.45, M.47
- Ligands: LDA.6, LDA.24
4 PLIP interactions:1 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:G.45
- Hydrophobic interactions: A:F.461, A:F.461, A:W.485
LMT.28: 10 residues within 4Å:- Chain A: F.356, A.360, W.363
- Chain B: F.77, L.81, F.100, H.102, N.103, W.110
- Ligands: LDA.23
10 PLIP interactions:7 interactions with chain B, 3 interactions with chain A- Hydrophobic interactions: B:F.77, B:L.81, B:F.100, B:F.100, B:W.110, A:F.356, A:A.360, A:W.363
- Hydrogen bonds: B:H.102, B:N.103
LMT.29: 10 residues within 4Å:- Chain B: W.62, L.116, V.119, A.120, F.124, I.128
- Chain D: E.27, N.28, Y.30
- Ligands: LDA.25
9 PLIP interactions:5 interactions with chain B, 4 interactions with chain D- Hydrophobic interactions: B:L.116, B:V.119, B:F.124, B:F.124
- Hydrogen bonds: B:R.131, D:E.27, D:N.28, D:N.28, D:N.28
- 1 x PER: PEROXIDE ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Durr, K.L. et al., A d-pathway mutation decouples the paracoccusdenitrificans cytochrome C oxidase by altering the side-chain orientation of a distant conserved glutamate. J.Mol.Biol. (2008)
- Release Date
- 2008-09-30
- Peptides
- Cytochrome c oxidase subunit 1-beta: A
Cytochrome c oxidase subunit 2: B
FV fragment Chain H: C
FV fragment Chain L: D - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.32 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 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)
- 9 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 12 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
- 1 x PER: PEROXIDE ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Durr, K.L. et al., A d-pathway mutation decouples the paracoccusdenitrificans cytochrome C oxidase by altering the side-chain orientation of a distant conserved glutamate. J.Mol.Biol. (2008)
- Release Date
- 2008-09-30
- Peptides
- Cytochrome c oxidase subunit 1-beta: A
Cytochrome c oxidase subunit 2: B
FV fragment Chain H: C
FV fragment Chain L: D - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D - Membrane
-
We predict this structure to be a membrane protein.