Research workbench
Crystal structure for the complex of human carbonic anhydrase IV and topiramate
Analyse Crystal structure for the complex of human carbonic anhydrase IV and topiramate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JNA
- Type
- protein
- Length
- 1,041 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbonic anhydrase 4
- EC
- 4.2.1.1
- UniProt
- P22748
- Ligands
- TOR, ZN, SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbonic anhydrase 4 (EC 4.2.1.1) | protein | 259 | 16% helix, 31% strand | P22748 |
| B | Carbonic anhydrase 4 (EC 4.2.1.1) | protein | 255 | 18% helix, 32% strand | P22748 |
| C | Carbonic anhydrase 4 (EC 4.2.1.1) | protein | 264 | 17% helix, 31% strand | P22748 |
| D | Carbonic anhydrase 4 (EC 4.2.1.1) | protein | 263 | 17% helix, 31% strand | P22748 |
Ligands and binding sites
- TOR · [(3aS,5aR,8aR,8bS)-2,2,7,7-tetramethyltetrahydro-3aH-bis[1,3]dioxolo[4,5-b:4',5'-d]pyran-3a-yl]methyl sulfamate · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 760 | 0.76 | 0.81 | 91 | GOL |
| 2 | 192 | 0.56 | 0.80 | 19 | empty |
| 3 | 176 | 0.54 | 0.79 | 22 | empty |
| 4 | 127 | 0.53 | 0.81 | 23 | TOR |
| 5 | 124 | 0.53 | 0.82 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 747 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 438 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 427 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 187 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 99 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5JNA · Crystal structure for the complex of human carbonic anhydrase IV and topiramate · the same entry in another collection · chain D against D, TM-score 1.00
- P22748 · AlphaFold monomer V2.0 prediction for carbonic anhydrase 4 (P22748) · a predicted model of the same protein · chain C 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 P22748
- Elsewhere: RCSB PDB 5JNA · PDBe 5JNA · UniProt P22748
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