MolNFT v1 · #39464 · protein
Escherichia COLI nucleoside diphosphate kinase
2HUR: “Escherichia COLI nucleoside diphosphate kinase”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.83). MolNFT v1 #39464 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2HUR
- Type
- protein
- Length
- 852 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- P0A763
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 142 | 41% helix, 20% strand | P0A763 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.83 | 0.84 | 67 | empty |
| 2 | 453 | 0.68 | 0.80 | 42 | empty |
| 3 | 193 | 0.49 | 0.76 | 28 | SO4 |
| 4 | 202 | 0.47 | 0.74 | 27 | SO4 |
| 5 | 152 | 0.44 | 0.76 | 25 | SO4 |
Interfaces
9 interfaces between chains.
- C–D · 1238 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1235 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1227 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 494 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 488 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 P0A763
- Elsewhere: RCSB PDB 2HUR · PDBe 2HUR · UniProt P0A763
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