MolNFT v1 · #135243 · protein
Crystal structure of the complex of helicobacter pylori alpha-carbonic anhydrase with benzolamide
5TT8: “Crystal structure of the complex of helicobacter pylori alpha-carbonic anhydrase with benzolamide”. X-ray diffraction, 3 ligands (D8W, ZN, CL), 19 pockets (best druggability 0.79). MolNFT v1 #135243 on GenesisL1: 3D structure…
- PDB
- 5TT8
- Type
- protein
- Length
- 1,725 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-carbonic anhydrase
- UniProt
- A0A0M3KL20
- Ligands
- D8W, ZN, CL
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 13% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-carbonic anhydrase | protein | 201 | 10% helix, 36% strand | A0A0M3KL20 |
| B | Alpha-carbonic anhydrase | protein | 221 | 14% helix, 39% strand | A0A0M3KL20 |
| C | Alpha-carbonic anhydrase | protein | 227 | 12% helix, 37% strand | A0A0M3KL20 |
| D | Alpha-carbonic anhydrase | protein | 196 | 9% helix, 38% strand | A0A0M3KL20 |
| E | Alpha-carbonic anhydrase | protein | 224 | 14% helix, 39% strand | A0A0M3KL20 |
| F | Alpha-carbonic anhydrase | protein | 216 | 12% helix, 40% strand | A0A0M3KL20 |
| G | Alpha-carbonic anhydrase | protein | 217 | 12% helix, 38% strand | A0A0M3KL20 |
| H | Alpha-carbonic anhydrase | protein | 223 | 16% helix, 38% strand | A0A0M3KL20 |
Ligands and binding sites
- D8W · 5-[(phenylsulfonyl)amino]-1,3,4-thiadiazole-2-sulfonamide · ligand · 7 copies · chains A, B, C, D, E, G, H
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 4 copies · chains A, B, C, E
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.79 | 0.81 | 100 | empty |
| 2 | 897 | 0.75 | 0.79 | 81 | empty |
| 3 | 59 | 0.72 | 0.99 | 23 | empty |
| 4 | 886 | 0.70 | 0.75 | 64 | empty |
| 5 | 53 | 0.64 | 0.94 | 20 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1363 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1331 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 1292 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1273 Ų buried · 20 hydrogen bonds · protein-protein
- A–F · 358 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5TT8 · Crystal structure of the complex of Helicobacter pylori alpha-carbonic anhydrase with… · the same entry in another collection · chain A 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 A0A0M3KL20
- Elsewhere: RCSB PDB 5TT8 · PDBe 5TT8 · UniProt A0A0M3KL20
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