MolNFT v1 · #111052 · protein
Crystal structure of RV1284 in the presence of polycarpine at acidic pH
4YF5 · Beta-carbonic anhydrase 1: “Crystal structure of RV1284 in the presence of polycarpine at acidic pH”. X-ray diffraction, 2 ligands (ZN, CL), 3 pockets (best druggability 0.63). MolNFT v1 #111052 on GenesisL1: 3D structure, binding…
- PDB
- 4YF5
- Type
- protein
- Length
- 652 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-carbonic anhydrase 1
- EC
- 4.2.1.1
- UniProt
- P9WPJ6
- Ligands
- ZN, CL
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-carbonic anhydrase 1 (EC 4.2.1.1) | protein | 163 | 39% helix, 18% strand | P9WPJ6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.63 | 0.76 | 56 | empty |
| 2 | 98 | 0.35 | 0.74 | 17 | empty |
| 3 | 87 | 0.35 | 0.75 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3884 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 3883 Ų buried · 60 hydrogen bonds · protein-protein
- B–C · 245 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 40 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4YF5 · Crystal structure of Rv1284 in the presence of polycarpine at acidic pH · the same entry in another collection · chain A against A, TM-score 1.00
- P9WPJ6 · AlphaFold monomer V2.0 prediction for beta-carbonic anhydrase 1 (P9WPJ6) · a predicted model of the same protein · chain A 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 P9WPJ6
- Elsewhere: RCSB PDB 4YF5 · PDBe 4YF5 · UniProt P9WPJ6
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