MolNFT v1 · #170914 · protein
Cytochrome C oxidase from saccharomyces cerevisiae
6YMY: “Cytochrome C oxidase from saccharomyces cerevisiae”. Electron microscopy, 7 ligands (PTY, PCF, HEA). MolNFT v1 #170914 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YMY
- Type
- protein
- Length
- 1,766 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P00401, P00410, P00420, P04037, P00424, P00427, P10174, P04039, P07255, Q01519, P32799, Q2V2P9
- Ligands
- PTY, PCF, HEA, CN3, CUA, CU, ZN
Structure
electron microscopy · 12 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | — | protein | 530 | — | P00401 |
| b | — | protein | 236 | — | P00410 |
| c | — | protein | 268 | — | P00420 |
| d | — | protein | 117 | — | P04037 |
| e | — | protein | 128 | — | P00424 |
| f | — | protein | 99 | — | P00427 |
| g | — | protein | 55 | — | P10174 |
| h | — | protein | 51 | — | P04039 |
| i | — | protein | 52 | — | P07255 |
| j | — | protein | 78 | — | Q01519 |
| k | — | protein | 114 | — | P32799 |
| m | — | protein | 38 | — | Q2V2P9 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 7 copies · chains a, b, e, c, i, m
- PCF · 1,2-diacyl-sn-glycero-3-phoshocholine · ligand · 3 copies · chains a, c, k, e, b, m
- HEA · Heme-A · ligand · 2 copies · chains a, b
- CN3 · (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate · ligand · chains a, e, h
- CUA · Dinuclear copper ion · ligand · chains b
- CU · Copper (II) ion · metal · chains a
- ZN · Zinc ion · metal · chains d
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 6YMY · Cytochrome c oxidase from Saccharomyces cerevisiae · the same entry in another collection · chain m against m, 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 P00401
- Every structure of UniProt P00410
- Every structure of UniProt P00420
- Every structure of UniProt P04037
- Every structure of UniProt P00424
- Every structure of UniProt P00427
- Every structure of UniProt P10174
- Every structure of UniProt P04039
- Every structure of UniProt P07255
- Every structure of UniProt Q01519
- Every structure of UniProt P32799
- Every structure of UniProt Q2V2P9
- Elsewhere: RCSB PDB 6YMY · PDBe 6YMY · UniProt P00401 · UniProt P00410 · UniProt P00420 · UniProt P04037 · UniProt P00424 · UniProt P00427 · UniProt P10174 · UniProt P04039 · UniProt P07255 · UniProt Q01519 · UniProt P32799 · UniProt Q2V2P9
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