Research workbench
Cytochrome C oxidase from saccharomyces cerevisiae
Analyse Cytochrome C oxidase from saccharomyces cerevisiae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YMY
- Type
- protein
- Length
- 1,766 residues
- Chains
- 12
- 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
- P00401, P00410, P00420, P04037, P00424, P00427, P10174, P04039, P07255, Q01519, P32799, Q2V2P9
- Ligands
- PTY, PCF, HEA, CN3, CUA, CU, ZN
- Pockets
- 20 · best druggability 0.91
Structure
electron microscopy · 12 distinct chains · 51% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 530 | 60% helix, 1% strand | P00401 |
| b | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 236 | 30% helix, 19% strand | P00410 |
| c | Cytochrome C oxidase subunit 3 (EC 1.9.3.1) | protein | 268 | 62% helix, 0% strand | P00420 |
| d | Cytochrome C oxidase subunit 4, mitochondrial | protein | 117 | 10% helix, 9% strand | P04037 |
| e | Cytochrome C oxidase subunit 5A, mitochondrial | protein | 128 | 47% helix, 0% strand | P00424 |
| f | Cytochrome C oxidase subunit 6, mitochondrial | protein | 99 | 65% helix, 0% strand | P00427 |
| g | Cytochrome C oxidase subunit 7, mitochondrial | protein | 55 | 67% helix, 0% strand | P10174 |
| h | Cytochrome C oxidase subunit 8, mitochondrial | protein | 51 | 49% helix, 0% strand | P04039 |
| i | Cytochrome C oxidase subunit 9, mitochondrial | protein | 52 | 73% helix, 0% strand | P07255 |
| j | Cytochrome C oxidase subunit 12, mitochondrial | protein | 78 | 40% helix, 0% strand | Q01519 |
| k | Cytochrome C oxidase subunit 13, mitochondrial | protein | 114 | 40% helix, 0% strand | P32799 |
| m | Cytochrome C oxidase subunit 26, mitochondrial | protein | 38 | 79% helix, 0% strand | Q2V2P9 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 7 copies · chains a, b, e, i, c, 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.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.91 | 0.93 | 96 | HEA |
| 2 | 857 | 0.83 | 0.85 | 75 | PTY |
| 3 | 142 | 0.81 | 0.97 | 24 | empty |
| 4 | 385 | 0.77 | 0.87 | 53 | empty |
| 5 | 656 | 0.75 | 0.81 | 62 | PTY |
Interfaces
34 interfaces between chains.
- a–b · 3726 Ų buried · 32 hydrogen bonds · protein-protein
- a–c · 2633 Ų buried · 18 hydrogen bonds · protein-protein
- a–h · 1797 Ų buried · 12 hydrogen bonds · protein-protein
- c–k · 1776 Ų buried · 13 hydrogen bonds · protein-protein
- a–e · 1689 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
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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