Research workbench
Structure of wild type amidase from vibrio cholerae 0395 at low temparature at 1.8 ångströms resolution.
Analyse Structure of wild type amidase from vibrio cholerae 0395 at low temparature at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JZM
- Type
- protein
- Length
- 1,686 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intracellular PROTEASE/AMIDASE
- EC
- 4.2.1.130
- UniProt
- A0A0H3AFW5
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Intracellular PROTEASE/AMIDASE (EC 4.2.1.130) | protein | 281 | 37% helix, 17% strand | A0A0H3AFW5 |
Pockets
15 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.76 | 0.83 | 63 | empty |
| 2 | 644 | 0.72 | 0.79 | 71 | empty |
| 3 | 173 | 0.68 | 0.87 | 36 | empty |
| 4 | 185 | 0.67 | 0.86 | 45 | empty |
| 5 | 360 | 0.61 | 0.78 | 52 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1086 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1084 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 913 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 470 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 384 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5JZM · Structure of wild type Amidase from Vibrio cholerae 0395 at low temparature at 1.8… · 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 A0A0H3AFW5
- Elsewhere: RCSB PDB 5JZM · PDBe 5JZM · UniProt A0A0H3AFW5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.