MolNFT v1 · #67101 · protein
Crystal structure of the catalytic domain of the tumor-associated human carbonic anhydrase IX
3IAI · Carbonic anhydrase 9: “Crystal structure of the catalytic domain of the tumor-associated human carbonic anhydrase IX”. X-ray diffraction, 6 ligands (AZM, NAG, MAN), 12 pockets (best druggability 0.85). MolNFT v1 #67101 on GenesisL1…
- PDB
- 3IAI
- Type
- protein
- Length
- 1,014 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbonic anhydrase 9
- EC
- 4.2.1.1
- UniProt
- Q16790
- Ligands
- AZM, NAG, MAN, BMA, ZN, PO4
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbonic anhydrase 9 (EC 4.2.1.1) | protein | 257 | 15% helix, 33% strand | Q16790 |
| B, C | Carbonic anhydrase 9 (EC 4.2.1.1) | protein | 252 | 15% helix, 35% strand | Q16790 |
| D | Carbonic anhydrase 9 (EC 4.2.1.1) | protein | 253 | 15% helix, 35% strand | Q16790 |
Ligands and binding sites
- AZM · 5-acetamido-1,3,4-thiadiazole-2-sulfonamide · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 5 copies · chains A, D, B, C
- GOL · Glycerol · additive · 25 copies · chains A, B, D, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.85 | 0.86 | 125 | PO4, GOL |
| 2 | 883 | 0.85 | 0.87 | 87 | empty |
| 3 | 461 | 0.68 | 0.80 | 40 | GOL |
| 4 | 497 | 0.68 | 0.79 | 50 | GOL |
| 5 | 215 | 0.57 | 0.79 | 23 | AZM, GOL |
Interfaces
5 interfaces between chains.
- A–B · 837 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 832 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 613 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 605 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 502 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3IAI · Crystal structure of the catalytic domain of the tumor-associated human carbonic… · the same entry in another collection · chain D against D, TM-score 1.00
- Q16790 · AlphaFold monomer V2.0 prediction for carbonic anhydrase 9 (Q16790) · 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 Q16790
- Elsewhere: RCSB PDB 3IAI · PDBe 3IAI · UniProt Q16790
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