MolNFT v1 · #55264 · protein
Structure of CAA3-type cytochrome oxidase
2YEV · Cytochrome C oxidase polypeptide I+III: “Structure of CAA3-type cytochrome oxidase”. X-ray diffraction, 10 ligands (HAS, 5PL, 7E8), 20 pockets (best druggability 0.89). MolNFT v1 #55264 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2YEV
- Type
- protein
- Length
- 2,325 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase polypeptide I+III; Cytochrome C oxidase subunit 2; CAA3-type…
- EC
- 1.9.3.1
- UniProt
- P98005, Q5SLI2, Q5SH67
- Ligands
- HAS, 5PL, 7E8, CUA, HEC, 4AG, 7E9, CU, MG, CL
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Cytochrome C oxidase polypeptide I+III (EC 1.9.3.1) | protein | 780 | 72% helix, 1% strand | P98005 |
| B, E | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 319 | 37% helix, 22% strand | Q5SLI2 |
| C | CAA3-type cytochrome oxidase subunit IV (EC 1.9.3.1) | protein | 64 | 80% helix, 0% strand | Q5SH67 |
| F | CAA3-type cytochrome oxidase subunit IV (EC 1.9.3.1) | protein | 63 | 84% helix, 0% strand | Q5SH67 |
Ligands and binding sites
- HAS · Heme-as · ligand · 4 copies · chains A, B, D, E
- 5PL · (1R,4S,6R)-6-({[2-(acetylamino)-2-deoxy-alpha-D-glucopyranosyl]oxy}methyl)-4-hydroxy-1-{[(15-methylhexadecanoyl)oxy]methyl}-4-oxido-7-oxo-3,5-dioxa-8-aza-4-phosphaheptacos-1-yl 15-methylhexadecanoate · ligand · 2 copies · chains A, D
- 7E8 · (2R)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate · ligand · 2 copies · chains A
- CUA · Dinuclear copper ion · ligand · 2 copies · chains B, E
- HEC · Heme C · ligand · 2 copies · chains B, E
- 4AG · (2R)-3-hydroxypropane-1,2-diyl dihexadecanoate · ligand · chains A, B
- 7E9 · 1,3-dihydroxypropan-2-yl (Z)-tetradec-7-enoate · ligand · chains B
- CU · Copper (II) ion · metal · 2 copies · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, D, E
- CL · Chloride ion · ion · 3 copies · chains A, C, D, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.89 | 0.90 | 111 | HAS |
| 2 | 1046 | 0.89 | 0.90 | 109 | HAS |
| 3 | 1155 | 0.87 | 0.88 | 103 | 5PL |
| 4 | 777 | 0.87 | 0.90 | 82 | 5PL |
| 5 | 1179 | 0.87 | 0.87 | 138 | HEC |
Interfaces
7 interfaces between chains.
- A–B · 3878 Ų buried · 41 hydrogen bonds · protein-protein
- D–E · 3856 Ų buried · 35 hydrogen bonds · protein-protein
- D–F · 1939 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1910 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 761 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 2 modified (heme c attachment, formylation).
Compared structures
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 P98005
- Every structure of UniProt Q5SLI2
- Every structure of UniProt Q5SH67
- Elsewhere: RCSB PDB 2YEV · PDBe 2YEV · UniProt P98005 · UniProt Q5SLI2 · UniProt Q5SH67
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