MolNFT v1 · #138128 · protein
Crystal structure of co-bound cytochrome C oxidase determined by serial femtosecond X-ray crystallography at room temperature
5W97 · Cytochrome C oxidase subunit 1: “Crystal structure of co-bound cytochrome C oxidase determined by serial femtosecond X-ray crystallography at…”. X-ray diffraction, 13 ligands (PGV, CHD, TGL), 20 pockets (best druggability 0.91).…
- PDB
- 5W97
- Type
- protein
- Length
- 3,558 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
- 1.9.3.1
- UniProt
- P00396, P68530, P00415, P00423, P00426, P00428, P07471, P00429, P04038, P07470, P13183, P00430, P10175
- Ligands
- PGV, CHD, TGL, PEK, HEA, CDL, CUA, PSC, CU, MG, NA, ZN, CMO
- 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, a | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 514 | 71% helix, 2% strand | P00396 |
| B, b | Cytochrome C oxidase subunit 2 | protein | 227 | 32% helix, 26% strand | P68530 |
| C, c | Cytochrome C oxidase subunit 3 | protein | 259 | 76% helix, 0% strand | P00415 |
| D, d | Cytochrome C oxidase subunit 4 isoform 1, mitochondrial | protein | 144 | 52% helix, 3% strand | P00423 |
| E, e | Cytochrome C oxidase subunit 5A, mitochondrial | protein | 105 | 65% helix, 1% strand | P00426 |
| F, f | Cytochrome C oxidase subunit 5B, mitochondrial | protein | 98 | 15% helix, 24% strand | P00428 |
| G, g | Cytochrome C oxidase subunit 6A2, mitochondrial | protein | 84 | 30% helix, 2% strand | P07471 |
| H, h | Cytochrome C oxidase subunit 6B1 | protein | 79 | 59% helix, 1% strand | P00429 |
| I, i | Cytochrome C oxidase subunit 6C | protein | 73 | 71% helix, 1% strand | P04038 |
| J, j | Cytochrome C oxidase subunit 7A1, mitochondrial | protein | 58 | 62% helix, 0% strand | P07470 |
| K, k | Cytochrome C oxidase subunit 7B, mitochondrial | protein | 49 | 61% helix, 0% strand | P13183 |
| L, l | Cytochrome C oxidase subunit 7C, mitochondrial | protein | 46 | 63% helix, 0% strand | P00430 |
| M, m | Cytochrome C oxidase subunit 8B, mitochondrial | protein | 43 | 65% helix, 5% 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, H, c, g, G, a, h, d, k, m, f
- CHD · Cholic acid · ligand · 8 copies · chains A, B, g, C, c, J, G, a, b, j
- TGL · Tristearoylglycerol · ligand · 6 copies · chains A, B, I, D, L, a, b, d, i, l
- 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, G, a, b, g, c, B
- HEA · Heme-A · ligand · 4 copies · chains A, B, a, b
- CDL · Cardiolipin · ligand · 4 copies · chains C, J, G, a, b, c, j, A, B, g
- CUA · Dinuclear copper ion · ligand · 2 copies · chains B, b
- 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, E, I, a, b, e, i
- CU · Copper (II) ion · metal · 2 copies · chains A, a
- MG · Magnesium ion · metal · 2 copies · chains A, B, a, b
- NA · Sodium ion · metal · 2 copies · chains A, a
- ZN · Zinc ion · metal · 2 copies · chains F, f
- CMO · Carbon monoxide · ion · 2 copies · chains A, a
- DMU · Decyl-beta-D-maltopyranoside · additive · 4 copies · chains C, G, A, D, L, M, c, g, a, d, l, m
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 | 1056 | 0.91 | 0.93 | 115 | HEA, CMO |
| 2 | 1149 | 0.91 | 0.93 | 129 | HEA, CMO |
| 3 | 746 | 0.86 | 0.88 | 80 | PGV |
| 4 | 721 | 0.85 | 0.88 | 82 | PGV |
| 5 | 978 | 0.84 | 0.85 | 112 | empty |
Interfaces
79 interfaces between chains.
- A–B · 3574 Ų buried · 32 hydrogen bonds · protein-protein
- a–b · 3535 Ų buried · 33 hydrogen bonds · protein-protein
- a–c · 2620 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 2610 Ų buried · 16 hydrogen bonds · protein-protein
- a–l · 1804 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 4 disulfide (disulfide, formylation, acetylation, phosphorylation).
Compared structures
- 5W97 · Crystal Structure of CO-bound Cytochrome c Oxidase determined by Serial Femtosecond X-Ray… · the same entry in another collection · chain K against K, 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 5W97 · PDBe 5W97 · 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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