Research workbench
Crystal structure of adenylate kinase from vibrio cholerae O1 biovar eltor
Analyse Crystal structure of adenylate kinase from vibrio cholerae O1 biovar eltor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NP6
- Type
- protein
- Length
- 858 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- Q9KTB7
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Adenylate kinase (EC 2.7.4.3) | protein | 216 | 49% helix, 18% strand | Q9KTB7 |
| B | Adenylate kinase (EC 2.7.4.3) | protein | 215 | 51% helix, 18% strand | Q9KTB7 |
| D | Adenylate kinase (EC 2.7.4.3) | protein | 211 | 49% helix, 18% strand | Q9KTB7 |
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.72 | 0.81 | 33 | empty |
| 2 | 436 | 0.70 | 0.81 | 32 | empty |
| 3 | 55 | 0.64 | 0.94 | 20 | empty |
| 4 | 384 | 0.57 | 0.74 | 58 | empty |
| 5 | 272 | 0.52 | 0.75 | 39 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1123 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1040 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 411 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 86 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4NP6 · Crystal Structure of Adenylate Kinase from Vibrio cholerae O1 biovar eltor · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KTB7 · AlphaFold monomer V2.0 prediction for adenylate kinase (Q9KTB7) · a predicted model of the same protein · chain D against A, TM-score 0.71
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 Q9KTB7
- Elsewhere: RCSB PDB 4NP6 · PDBe 4NP6 · UniProt Q9KTB7
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