MolNFT v1 · #97781 · protein
Crystal structure of the nucleoside diphosphate kinase B from leishmania braziliensis
4KPC: “Crystal structure of the nucleoside diphosphate kinase B from leishmania braziliensis”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.49). MolNFT v1 #97781 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4KPC
- Type
- protein
- Length
- 279 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase B
- EC
- 2.7.4.6
- UniProt
- A4HKT8
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside diphosphate kinase B (EC 2.7.4.6) | protein | 141 | 44% helix, 17% strand | A4HKT8 |
| B | Nucleoside diphosphate kinase B (EC 2.7.4.6) | protein | 138 | 45% helix, 17% strand | A4HKT8 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.49 | 0.77 | 23 | PO4 |
| 2 | 181 | 0.47 | 0.76 | 25 | PO4 |
| 3 | 88 | 0.35 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 746 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4KPC · Crystal structure of the nucleoside diphosphate kinase b from Leishmania braziliensis · 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 A4HKT8
- Elsewhere: RCSB PDB 4KPC · PDBe 4KPC · UniProt A4HKT8
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