MolNFT v1 · #170422 · protein
X-ray crystal structure of human carbonic anhydrase IX catalytic domain.
6Y74 · Carbonic anhydrase 9: “X-ray crystal structure of human carbonic anhydrase IX catalytic domain.”. X-ray diffraction, 4 ligands (NAG, BMA, ZN), 4 pockets (best druggability 0.60). MolNFT v1 #170422 on GenesisL1: 3D structure, binding…
- PDB
- 6Y74
- Type
- protein
- Length
- 516 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbonic anhydrase 9
- EC
- 4.2.1.1
- UniProt
- Q16790
- Ligands
- NAG, BMA, ZN, CL
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carbonic anhydrase 9 (EC 4.2.1.1) | protein | 258 | 16% helix, 34% strand | Q16790 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.60 | 0.78 | 35 | ACT |
| 2 | 298 | 0.59 | 0.78 | 32 | ZN, ACT |
| 3 | 54 | 0.35 | 0.79 | 13 | empty |
| 4 | 54 | 0.32 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 643 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6Y74 · X-ray crystal structure of human carbonic anhydrase IX catalytic domain. · the same entry in another collection · chain A against A, TM-score 1.00
- Q16790 · AlphaFold monomer V2.0 prediction for carbonic anhydrase 9 (Q16790) · 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 Q16790
- Elsewhere: RCSB PDB 6Y74 · PDBe 6Y74 · UniProt Q16790
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