Research workbench
Crystal structure of human carbonic anhydrase isozyme xiii with inhibitor
Analyse Crystal structure of human carbonic anhydrase isozyme xiii with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QJP
- Type
- protein
- Length
- 516 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbonic anhydrase 13
- EC
- 4.2.1.1
- UniProt
- Q8N1Q1
- Ligands
- V1F, ZN
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Carbonic anhydrase 13 (EC 4.2.1.1) | protein | 258 | 16% helix, 32% strand | Q8N1Q1 |
Ligands and binding sites
- V1F · 3-(benzylamino)-2,5,6-trifluoro-4-[(2-phenylethyl)sulfonyl]benzenesulfonamide · ligand · 2 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 4 copies · chains B, A
- PEG · Di(hydroxyethyl)ether · additive · chains B
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.68 | 0.85 | 36 | empty |
| 2 | 201 | 0.58 | 0.80 | 30 | V1F |
| 3 | 200 | 0.57 | 0.80 | 27 | V1F |
| 4 | 113 | 0.44 | 0.78 | 25 | empty |
| 5 | 55 | 0.28 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- B–A · 709 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4QJP · Crystal structure of human carbonic anhydrase isozyme XIII with inhibitor · the same entry in another collection · chain B against B, TM-score 1.00
- Q8N1Q1 · AlphaFold monomer V2.0 prediction for carbonic anhydrase 13 (Q8N1Q1) · 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 Q8N1Q1
- Elsewhere: RCSB PDB 4QJP · PDBe 4QJP · UniProt Q8N1Q1
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