MolNFT v1 · #140857 · protein
Crystal structure of octameric form of nucleoside diphosphate kinase from acinetobacter baumannii at 2.2 a resolution
5YOL: “Crystal structure of octameric form of nucleoside diphosphate kinase from acinetobacter baumannii at 2.2 a…”. X-ray diffraction, 1 ligand (MG), 14 pockets (best druggability 0.83). MolNFT v1 #140857 on GenesisL1: 3D structure…
- PDB
- 5YOL
- Type
- protein
- Length
- 1,144 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- V5VIC4
- Ligands
- MG
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 143 | 45% helix, 20% strand | V5VIC4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 12 copies · chains A, G, B, F, C, E, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.83 | 0.84 | 85 | MG |
| 2 | 1120 | 0.81 | 0.82 | 91 | MG |
| 3 | 765 | 0.72 | 0.78 | 65 | empty |
| 4 | 763 | 0.70 | 0.77 | 64 | empty |
| 5 | 217 | 0.50 | 0.76 | 24 | empty |
Interfaces
17 interfaces between chains.
- B–C · 1228 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1228 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1223 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1222 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 508 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5YOL · Crystal structure of octameric form of Nucleoside diphosphate kinase from Acinetobacter… · 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 V5VIC4
- Elsewhere: RCSB PDB 5YOL · PDBe 5YOL · UniProt V5VIC4
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