Research workbench
Crystal structure of RV1284 in the presence of polycarpine at mildly acidic pH
Analyse Crystal structure of RV1284 in the presence of polycarpine at mildly acidic pH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YF4
- 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, MG, CL
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 37% 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 | 37% helix, 18% strand | P9WPJ6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- 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 | 497 | 0.64 | 0.76 | 56 | empty |
| 2 | 87 | 0.34 | 0.74 | 14 | empty |
| 3 | 87 | 0.33 | 0.74 | 15 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3880 Ų buried · 57 hydrogen bonds · protein-protein
- A–B · 3872 Ų buried · 63 hydrogen bonds · protein-protein
- B–C · 274 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 45 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YF4 · Crystal structure of Rv1284 in the presence of polycarpine at mildly acidic pH · the same entry in another collection · chain B against B, 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 4YF4 · PDBe 4YF4 · UniProt P9WPJ6
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