Research workbench
Three dimensional structure of human carbonic anhydrase IX in complex with sulfonamide
Analyse Three dimensional structure of human carbonic anhydrase IX in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G98
- Type
- protein
- Length
- 962 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
- ER5, ZN
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbonic anhydrase 9 (EC 4.2.1.1) | protein | 241 | 15% helix, 35% strand | Q16790 |
| B | Carbonic anhydrase 9 (EC 4.2.1.1) | protein | 243 | 14% helix, 34% strand | Q16790 |
| C, D | Carbonic anhydrase 9 (EC 4.2.1.1) | protein | 239 | 15% helix, 36% strand | Q16790 |
Ligands and binding sites
- ER5 · 4-[2-[3-(cyclododecylamino)-2,5,6-tris(fluoranyl)-4-sulfamoyl-phenyl]sulfanylethyl]benzoic acid · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.84 | 0.93 | 44 | empty |
| 2 | 347 | 0.84 | 0.93 | 40 | empty |
| 3 | 124 | 0.71 | 0.92 | 33 | empty |
| 4 | 91 | 0.66 | 0.92 | 23 | empty |
| 5 | 254 | 0.55 | 0.77 | 35 | ER5 |
Interfaces
5 interfaces between chains.
- A–B · 897 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 868 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 439 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 422 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 291 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6G98 · Three dimensional structure of human carbonic anhydrase IX in complex with sulfonamide · 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 1.00
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 6G98 · PDBe 6G98 · UniProt Q16790
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