MolNFT v1 · #72715 · protein
Structure of leishmania ndkb complexed with AMP.
3NGT · Nucleoside diphosphate kinase: “Structure of leishmania ndkb complexed with AMP.”. X-ray diffraction, 1 ligand (AMP), 20 pockets (best druggability 0.84). MolNFT v1 #72715 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3NGT
- Type
- protein
- Length
- 2,063 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- Q9U1E1
- Ligands
- AMP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F, I, N | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 150 | 48% helix, 16% strand | Q9U1E1 |
| B, C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 148 | 50% helix, 16% strand | Q9U1E1 |
| G, K, M | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 149 | 45% helix, 16% strand | Q9U1E1 |
| H | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 147 | 43% helix, 16% strand | Q9U1E1 |
| J | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 148 | 48% helix, 16% strand | Q9U1E1 |
| L | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 125 | 38% helix, 19% strand | Q9U1E1 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 13 copies · chains A, E, B, F, C, D, G, K, H, I, J, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.84 | 0.89 | 77 | empty |
| 2 | 555 | 0.83 | 0.89 | 78 | empty |
| 3 | 519 | 0.83 | 0.89 | 65 | empty |
| 4 | 439 | 0.82 | 0.89 | 57 | empty |
| 5 | 402 | 0.82 | 0.90 | 52 | empty |
Interfaces
28 interfaces between chains.
- D–E · 1008 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 1001 Ų buried · 14 hydrogen bonds · protein-protein
- M–N · 993 Ų buried · 17 hydrogen bonds · protein-protein
- I–L · 991 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 989 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3NGT · Structure of Leishmania NDKb complexed with AMP. · 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 Q9U1E1
- Elsewhere: RCSB PDB 3NGT · PDBe 3NGT · UniProt Q9U1E1
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