Research workbench
CVAA9A
Analyse CVAA9A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NLT
- Type
- protein
- Length
- 1,351 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CVAA9A
- EC
- 1.-.-.-
- Ligands
- CU, SO4
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | CVAA9A (EC 1.-.-.-) | protein | 224 | 7% helix, 32% strand | — |
| B | CVAA9A (EC 1.-.-.-) | protein | 227 | 7% helix, 32% strand | — |
| C, E | CVAA9A (EC 1.-.-.-) | protein | 226 | 7% helix, 32% strand | — |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 8 copies · chains B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.75 | 0.82 | 52 | empty |
| 2 | 403 | 0.68 | 0.81 | 45 | empty |
| 3 | 260 | 0.51 | 0.75 | 38 | empty |
| 4 | 63 | 0.44 | 0.82 | 17 | empty |
| 5 | 133 | 0.42 | 0.75 | 18 | empty |
Interfaces
7 interfaces between chains.
- A–B · 463 Ų buried · 3 hydrogen bonds · protein-protein
- C–F · 443 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 442 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 401 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 259 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 modified (disulfide, methylation).
Compared structures
- 5NLT · CvAA9A · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 5NLT · PDBe 5NLT
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