MolNFT v1 · #128003 · protein
Structure of BA3-type cytochrome C oxidase from thermus thermophilus by serial femtosecond crystallography
5NDC · Cytochrome C oxidase subunit 1: “Structure of BA3-type cytochrome C oxidase from thermus thermophilus by serial femtosecond crystallography”. X-ray diffraction, 4 ligands (HEM, HAS, CUA), 4 pockets (best druggability 0.90). MolNFT…
- PDB
- 5NDC
- Type
- protein
- Length
- 752 residues
- Chains
- 3
- 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
- Q5SJ79, Q5SJ80, A0A1J1EEV7
- Ligands
- HEM, HAS, CUA, CU
- Pockets
- 4 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 554 | 73% helix, 2% strand | Q5SJ79 |
| B | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 167 | 28% helix, 35% strand | Q5SJ80 |
| C | Cytochrome C oxidase polypeptide iia | protein | 31 | 87% helix, 0% strand | A0A1J1EEV7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- HAS · Heme-as · ligand · chains A, C
- CUA · Dinuclear copper ion · ligand · chains B
- CU · Copper (II) ion · metal · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 15 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.90 | 0.91 | 135 | HEM, HAS |
| 2 | 109 | 0.37 | 0.74 | 16 | empty |
| 3 | 65 | 0.33 | 0.76 | 12 | empty |
| 4 | 58 | 0.28 | 0.73 | 13 | OLC |
Interfaces
3 interfaces between chains.
- A–B · 2963 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 1029 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 823 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5NDC · Structure of ba3-type cytochrome c oxidase from Thermus thermophilus by serial… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SJ79 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 1 (Q5SJ79) · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q5SJ80 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 2 (Q5SJ80) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q5SJ79
- Every structure of UniProt Q5SJ80
- Every structure of UniProt A0A1J1EEV7
- Elsewhere: RCSB PDB 5NDC · PDBe 5NDC · UniProt Q5SJ79 · UniProt Q5SJ80 · UniProt A0A1J1EEV7
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