MolNFT v1 · #111093 · protein
Crystal structure of the complex of helicobacter pylori alpha-carbonic anhydrase with acetazolamide
4YGF: “Crystal structure of the complex of helicobacter pylori alpha-carbonic anhydrase with acetazolamide”. X-ray diffraction, 3 ligands (AZM, ZN, CL), 16 pockets (best druggability 0.81). MolNFT v1 #111093 on GenesisL1: 3D structure…
- PDB
- 4YGF
- Type
- protein
- Length
- 1,804 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-carbonic anhydrase
- UniProt
- K4NGD4
- Ligands
- AZM, ZN, CL
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 15% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Alpha-carbonic anhydrase | protein | 226 | 17% helix, 38% strand | K4NGD4 |
| B | Alpha-carbonic anhydrase | protein | 223 | 16% helix, 38% strand | K4NGD4 |
| C | Alpha-carbonic anhydrase | protein | 227 | 15% helix, 37% strand | K4NGD4 |
| D | Alpha-carbonic anhydrase | protein | 224 | 14% helix, 36% strand | K4NGD4 |
| F, H | Alpha-carbonic anhydrase | protein | 225 | 15% helix, 38% strand | K4NGD4 |
| G | Alpha-carbonic anhydrase | protein | 228 | 14% helix, 39% strand | K4NGD4 |
Ligands and binding sites
- AZM · 5-acetamido-1,3,4-thiadiazole-2-sulfonamide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 5 copies · chains A, C, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.81 | 0.82 | 111 | empty |
| 2 | 931 | 0.75 | 0.79 | 102 | empty |
| 3 | 802 | 0.69 | 0.76 | 59 | empty |
| 4 | 188 | 0.59 | 0.82 | 24 | AZM, GOL |
| 5 | 178 | 0.59 | 0.82 | 25 | AZM, GOL |
Interfaces
12 interfaces between chains.
- C–D · 1333 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1330 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 1319 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1192 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 426 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4YGF · 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 K4NGD4
- Elsewhere: RCSB PDB 4YGF · PDBe 4YGF · UniProt K4NGD4
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