MolNFT v1 · #141395 · protein
Structure of human cytochrome C oxidase
5Z62 · Cytochrome C oxidase subunit 1: “Structure of human cytochrome C oxidase”. Electron microscopy, 6 ligands (PEE, HEA, CDL), 20 pockets (best druggability 0.88). MolNFT v1 #141395 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5Z62
- Type
- protein
- Length
- 1,855 residues
- Chains
- 14
- Method
- electron microscopy
- 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
- P00395, P00403, P00414, P13073, P20674, P10606, P12074, P14854, P09669, P14406, P24311, P15954, P10176, O00483
- Ligands
- PEE, HEA, CDL, CU, MG, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 14 distinct chains · 55% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 513 | 68% helix, 1% strand | P00395 |
| B | Cytochrome C oxidase subunit 2 | protein | 227 | 26% helix, 26% strand | P00403 |
| C | Cytochrome C oxidase subunit 3 | protein | 260 | 71% helix, 0% strand | P00414 |
| D | Cytochrome C oxidase subunit 4 isoform 1, mitochondrial | protein | 144 | 49% helix, 3% strand | P13073 |
| E | Cytochrome C oxidase subunit 5A, mitochondrial | protein | 109 | 61% helix, 1% strand | P20674 |
| F | Cytochrome C oxidase subunit 5B, mitochondrial | protein | 98 | 14% helix, 29% strand | P10606 |
| G | Cytochrome C oxidase subunit 6A1, mitochondrial | protein | 75 | 25% helix, 0% strand | P12074 |
| H | Cytochrome C oxidase subunit 6B1 | protein | 82 | 57% helix, 0% strand | P14854 |
| I | Cytochrome C oxidase subunit 6C | protein | 73 | 70% helix, 1% strand | P09669 |
| J | Cytochrome C oxidase subunit 7A2, mitochondrial | protein | 56 | 68% helix, 0% strand | P14406 |
| K | Cytochrome C oxidase subunit 7B, mitochondrial | protein | 49 | 55% helix, 0% strand | P24311 |
| L | Cytochrome C oxidase subunit 7C, mitochondrial | protein | 47 | 57% helix, 0% strand | P15954 |
| M | Cytochrome C oxidase subunit 8A, mitochondrial | protein | 43 | 67% helix, 2% strand | P10176 |
| N | Cytochrome C oxidase subunit NDUFA4 | protein | 79 | 43% helix, 0% strand | O00483 |
Ligands and binding sites
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 3 copies · chains A, C, G
- HEA · Heme-A · ligand · 2 copies · chains A, B
- CDL · Cardiolipin · ligand · chains A, C, N
- CU · Copper (II) ion · metal · 3 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- ZN · Zinc ion · metal · chains F
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 | 563 | 0.88 | 0.93 | 77 | HEA |
| 2 | 506 | 0.87 | 0.93 | 59 | MG, HEA |
| 3 | 977 | 0.86 | 0.87 | 93 | empty |
| 4 | 952 | 0.84 | 0.85 | 90 | PEE |
| 5 | 1077 | 0.80 | 0.81 | 88 | CDL |
Interfaces
39 interfaces between chains.
- A–B · 3537 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 2530 Ų buried · 12 hydrogen bonds · protein-protein
- A–L · 1729 Ų buried · 16 hydrogen bonds · protein-protein
- C–G · 1552 Ų buried · 9 hydrogen bonds · protein-protein
- B–I · 1433 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5Z62 · Structure of human cytochrome c oxidase · 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 P00395
- Every structure of UniProt P00403
- Every structure of UniProt P00414
- Every structure of UniProt P13073
- Every structure of UniProt P20674
- Every structure of UniProt P10606
- Every structure of UniProt P12074
- Every structure of UniProt P14854
- Every structure of UniProt P09669
- Every structure of UniProt P14406
- Every structure of UniProt P24311
- Every structure of UniProt P15954
- Every structure of UniProt P10176
- Every structure of UniProt O00483
- Elsewhere: RCSB PDB 5Z62 · PDBe 5Z62 · UniProt P00395 · UniProt P00403 · UniProt P00414 · UniProt P13073 · UniProt P20674 · UniProt P10606 · UniProt P12074 · UniProt P14854 · UniProt P09669 · UniProt P14406 · UniProt P24311 · UniProt P15954 · UniProt P10176 · UniProt O00483
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