Research workbench
Crystal structure of the complex of helicobacter pylori alpha-carbonic anhydrase with (E)-5-(((4-(tert-BUTYL)PHENYL)SULFONYL)IMINO)-4- methyl-4,5-dihydro-1,3,4-thiadiazole-2-sulfonamide
Analyse Crystal structure of the complex of helicobacter pylori alpha-carbonic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TV3
- Type
- protein
- Length
- 1,784 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-carbonic anhydrase
- EC
- 4.2.1.1
- UniProt
- A0A0M3KL20
- Ligands
- 7L3, ZN, CL
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Alpha-carbonic anhydrase (EC 4.2.1.1) | protein | 226 | 11% helix, 37% strand | A0A0M3KL20 |
| B | Alpha-carbonic anhydrase (EC 4.2.1.1) | protein | 218 | 13% helix, 42% strand | A0A0M3KL20 |
| C, H | Alpha-carbonic anhydrase (EC 4.2.1.1) | protein | 225 | 9% helix, 38% strand | A0A0M3KL20 |
| D | Alpha-carbonic anhydrase (EC 4.2.1.1) | protein | 220 | 12% helix, 36% strand | A0A0M3KL20 |
| F | Alpha-carbonic anhydrase (EC 4.2.1.1) | protein | 222 | 10% helix, 36% strand | A0A0M3KL20 |
| G | Alpha-carbonic anhydrase (EC 4.2.1.1) | protein | 222 | 12% helix, 39% strand | A0A0M3KL20 |
Ligands and binding sites
- 7L3 · (5Z)-5-{[(4-tert-butylphenyl)sulfonyl]imino}-4-methyl-4,5-dihydro-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 · 2 copies · chains D, G
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.74 | 0.77 | 78 | empty |
| 2 | 706 | 0.73 | 0.80 | 49 | empty |
| 3 | 83 | 0.73 | 0.95 | 25 | empty |
| 4 | 884 | 0.70 | 0.76 | 64 | empty |
| 5 | 580 | 0.63 | 0.75 | 50 | empty |
Interfaces
13 interfaces between chains.
- C–D · 1384 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1334 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 1304 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1197 Ų buried · 23 hydrogen bonds · protein-protein
- A–F · 507 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5TV3 · 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 5TV3 · PDBe 5TV3 · UniProt A0A0M3KL20
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