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Crystal structure of a chimeric cua domain (subunit II) of cytochrome BA3 from thermus thermophilus with the amicyanin loop
Analyse Crystal structure of a chimeric cua domain (subunit II) of cytochrome BA3 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U7N
- Type
- protein
- Length
- 908 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase subunit 2
- EC
- 1.9.3.1
- UniProt
- P98052
- Ligands
- CU
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 3% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 115 | 3% helix, 53% strand | P98052 |
| B, C | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 116 | 3% helix, 53% strand | P98052 |
| D, H | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 114 | 3% helix, 54% strand | P98052 |
| E | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 113 | 3% helix, 53% strand | P98052 |
| F | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 109 | 3% helix, 54% strand | P98052 |
| G | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 111 | 3% helix, 53% strand | P98052 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B, C, H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.79 | 0.81 | 73 | empty |
| 2 | 244 | 0.60 | 0.80 | 49 | empty |
| 3 | 217 | 0.54 | 0.78 | 36 | empty |
| 4 | 225 | 0.52 | 0.76 | 33 | empty |
| 5 | 94 | 0.49 | 0.82 | 19 | empty |
Interfaces
13 interfaces between chains.
- B–G · 741 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 709 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 693 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 410 Ų buried · 6 hydrogen bonds · protein-protein
- C–H · 298 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5U7N · Crystal structure of a chimeric cua domain (subunit II) of cytochrome BA3 from thermus… · the same entry in another collection · chain H against H, TM-score 1.00
- P98052 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 2 (P98052) · a predicted model of the same protein · chain H 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 P98052
- Elsewhere: RCSB PDB 5U7N · PDBe 5U7N · UniProt P98052
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