Research workbench
Bovine heart cytochrome C oxidase in a catalytic intermediate of O at 1.84 ångström resolution
Analyse Bovine heart cytochrome C oxidase in a catalytic intermediate of O at 1.84… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D5W
- Type
- protein
- Length
- 3,550 residues
- Chains
- 26
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase subunit 1; Cytochrome C oxidase subunit 2; Cytochrome C oxidase…
- EC
- 7.1.1.9
- UniProt
- P00396, P68530, P00415, P00423, P00426, P00428, P07471, P00429, P04038, P07470, P13183, P00430, P10175
- Ligands
- PGV, CHD, TGL, PEK, HEA, CDL, PSC, CUA, NA, CU, MG, ZN, PER, PO4
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 13 distinct chains · 59% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, N | Cytochrome C oxidase subunit 1 (EC 7.1.1.9) | protein | 514 | 72% helix, 1% strand | P00396 |
| B, O | Cytochrome C oxidase subunit 2 (EC 7.1.1.9) | protein | 227 | 35% helix, 26% strand | P68530 |
| C, P | Cytochrome C oxidase subunit 3 (EC 7.1.1.9) | protein | 259 | 76% helix, 0% strand | P00415 |
| D, Q | Cytochrome C oxidase subunit 4 isoform 1, mitochondrial | protein | 144 | 52% helix, 3% strand | P00423 |
| E, R | Cytochrome C oxidase subunit 5A, mitochondrial | protein | 105 | 64% helix, 1% strand | P00426 |
| F, S | Cytochrome C oxidase subunit 5B, mitochondrial | protein | 94 | 16% helix, 28% strand | P00428 |
| G, T | Cytochrome C oxidase subunit 6A2, mitochondrial | protein | 84 | 31% helix, 2% strand | P07471 |
| H, U | Cytochrome C oxidase subunit 6B1 | protein | 79 | 61% helix, 1% strand | P00429 |
| I, V | Cytochrome C oxidase subunit 6C | protein | 73 | 70% helix, 1% strand | P04038 |
| J, W | Cytochrome C oxidase subunit 7A1, mitochondrial | protein | 58 | 67% helix, 0% strand | P07470 |
| K, X | Cytochrome C oxidase subunit 7B, mitochondrial | protein | 49 | 55% helix, 0% strand | P13183 |
| L, Y | Cytochrome C oxidase subunit 7C, mitochondrial | protein | 46 | 59% helix, 0% strand | P00430 |
| M, Z | Cytochrome C oxidase subunit 8B, mitochondrial | protein | 43 | 67% helix, 2% strand | P10175 |
Ligands and binding sites
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 8 copies · chains A, D, K, M, C, F, P, T, N, Q, X, Z, S, G
- CHD · Cholic acid · ligand · 8 copies · chains A, B, T, C, P, J, G, N, O, L, M, Y, Z
- TGL · Tristearoylglycerol · ligand · 6 copies · chains A, B, I, D, L, N, O, V, Y, Q
- PEK · (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(stearoyloxy)methyl]ethyl (5E,8E,11E,14E)-icosa-5,8, 11,14-tetraenoate · ligand · 6 copies · chains A, C, T, G, N, P, B
- HEA · Heme-A · ligand · 4 copies · chains A, B, N, O
- CDL · Cardiolipin · ligand · 4 copies · chains C, J, G, N, O, P, W, A, B, T
- PSC · (7R,17E,20E)-4-hydroxy-N,N,N-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosa-17,20-dien-1-aminium 4-oxide · ligand · 2 copies · chains A, B, I, N, O, V
- CUA · Dinuclear copper ion · ligand · 2 copies · chains B, O
- NA · Sodium ion · metal · 4 copies · chains A, C, N, P
- CU · Copper (II) ion · metal · 2 copies · chains A, N
- MG · Magnesium ion · metal · 2 copies · chains A, B, N, O
- ZN · Zinc ion · metal · 2 copies · chains F, S
- PER · Peroxide ion · ion · 2 copies · chains A, N
- PO4 · Phosphate ion · ion · 2 copies · chains H, U
- EDO · 1,2-ethanediol · additive · 80 copies · chains A, D, M, B, F, C, G, H, J, K, E, S, L, N, Q, P, Z, O, T, U, W, Y
- DMU · Decyl-beta-D-maltopyranoside · additive · 23 copies · chains A, C, J, G, D, K, B, L, M, O, N, P, W, T, Q, X, Y, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.91 | 0.93 | 132 | HEA, PER, PSC |
| 2 | 1198 | 0.91 | 0.93 | 137 | HEA, PER, PSC |
| 3 | 784 | 0.86 | 0.89 | 85 | PGV |
| 4 | 1030 | 0.86 | 0.86 | 79 | PGV |
| 5 | 1028 | 0.84 | 0.85 | 99 | EDO |
Interfaces
80 interfaces between chains.
- A–B · 3628 Ų buried · 38 hydrogen bonds · protein-protein
- N–O · 3605 Ų buried · 38 hydrogen bonds · protein-protein
- N–P · 2651 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 2627 Ų buried · 17 hydrogen bonds · protein-protein
- A–L · 1742 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 4 disulfide (disulfide, formylation, acetylation).
Compared structures
- 7D5W · Bovine heart cytochrome c oxidase in a catalytic intermediate of O at 1.84 angstrom… · the same entry in another collection · chain J against J, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00396
- Every structure of UniProt P68530
- Every structure of UniProt P00415
- Every structure of UniProt P00423
- Every structure of UniProt P00426
- Every structure of UniProt P00428
- Every structure of UniProt P07471
- Every structure of UniProt P00429
- Every structure of UniProt P04038
- Every structure of UniProt P07470
- Every structure of UniProt P13183
- Every structure of UniProt P00430
- Every structure of UniProt P10175
- Elsewhere: RCSB PDB 7D5W · PDBe 7D5W · UniProt P00396 · UniProt P68530 · UniProt P00415 · UniProt P00423 · UniProt P00426 · UniProt P00428 · UniProt P07471 · UniProt P00429 · UniProt P04038 · UniProt P07470 · UniProt P13183 · UniProt P00430 · UniProt P10175
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