Research workbench
Vibrio cholerae PARA2-ADP
Analyse Vibrio cholerae PARA2-ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NPE
- Type
- protein
- Length
- 1,601 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aaa family ATPase
- UniProt
- A0A085S0Z4
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aaa family ATPase | protein | 397 | 49% helix, 10% strand | A0A085S0Z4 |
| B | Aaa family ATPase | protein | 402 | 49% helix, 10% strand | A0A085S0Z4 |
| C | Aaa family ATPase | protein | 400 | 48% helix, 11% strand | A0A085S0Z4 |
| D | Aaa family ATPase | protein | 402 | 48% helix, 9% strand | A0A085S0Z4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.73 | 0.76 | 112 | ADP, MG |
| 2 | 1199 | 0.72 | 0.76 | 119 | ADP, MG |
| 3 | 757 | 0.72 | 0.78 | 69 | GOL |
| 4 | 66 | 0.64 | 0.93 | 22 | empty |
| 5 | 285 | 0.63 | 0.80 | 52 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3081 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2848 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 504 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 22 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 15 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7NPE · Vibrio cholerae ParA2-ADP · the same entry in another collection · chain B against B, 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 A0A085S0Z4
- Elsewhere: RCSB PDB 7NPE · PDBe 7NPE · UniProt A0A085S0Z4
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