Research workbench
X-ray structure of human carbonic anhydrase 13 in complex with inhibitor
Analyse X-ray structure of human carbonic anhydrase 13 in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DA2
- Type
- protein
- Length
- 519 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
- 4MD, ZN, CL
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbonic anhydrase 13 (EC 4.2.1.1) | protein | 262 | 13% helix, 31% strand | Q8N1Q1 |
| B | Carbonic anhydrase 13 (EC 4.2.1.1) | protein | 257 | 16% helix, 30% strand | Q8N1Q1 |
Ligands and binding sites
- 4MD · N-(4-chlorobenzyl)-N-methylbenzene-1,4-disulfonamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.80 | 0.81 | 104 | ZN, 4MD |
| 2 | 178 | 0.57 | 0.81 | 24 | ZN, 4MD |
| 3 | 63 | 0.40 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 613 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3DA2 · X-ray structure of human carbonic anhydrase 13 in complex with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N1Q1 · AlphaFold monomer V2.0 prediction for carbonic anhydrase 13 (Q8N1Q1) · a predicted model of the same protein · chain B 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 3DA2 · PDBe 3DA2 · UniProt Q8N1Q1
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