Research workbench
Three dimensional structure of human carbonic anhydrase IX in complex with 5-(1-naphthalen-1-yl-1,2,3-triazol-4-YL)THIOPHENE-2-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
- 5FL4
- Type
- protein
- Length
- 1,004 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
- 9FK, ZN
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Carbonic anhydrase 9 (EC 4.2.1.1) | protein | 251 | 14% helix, 33% strand | Q16790 |
Ligands and binding sites
- 9FK · 5-(1-naphthalen-1-yl-1,2,3-triazol-4-yl)thiophene-2-sulfonamide · ligand · 4 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.86 | 0.91 | 73 | empty |
| 2 | 596 | 0.86 | 0.91 | 68 | ACY |
| 3 | 213 | 0.74 | 0.89 | 38 | empty |
| 4 | 92 | 0.62 | 0.89 | 24 | 9FK, GOL |
| 5 | 88 | 0.62 | 0.88 | 21 | 9FK, GOL |
Interfaces
5 interfaces between chains.
- C–D · 840 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 818 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 445 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 433 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 238 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5FL4 · Three dimensional structure of human carbonic anhydrase IX in complex with… · 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 D 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 5FL4 · PDBe 5FL4 · UniProt Q16790
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