MolNFT v1 · #136081 · protein
Structure of NME1 covalently conjugated to imidazole fluorosulfate
5UI4 · Nucleoside diphosphate kinase a: “Structure of NME1 covalently conjugated to imidazole fluorosulfate”. X-ray diffraction, 1 ligand (A7Z), 14 pockets (best druggability 0.89). MolNFT v1 #136081 on GenesisL1: 3D structure, binding…
- PDB
- 5UI4
- Type
- protein
- Length
- 896 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase a
- EC
- 2.7.4.6
- UniProt
- P15531
- Ligands
- A7Z
- Pockets
- 14 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F | Nucleoside diphosphate kinase a (EC 2.7.4.6) | protein | 149 | 47% helix, 16% strand | P15531 |
| B, D | Nucleoside diphosphate kinase a (EC 2.7.4.6) | protein | 150 | 47% helix, 16% strand | P15531 |
Ligands and binding sites
- A7Z · 4-[4-(3-methoxyphenyl)-1-(prop-2-yn-1-yl)-1H-imidazol-5-yl]phenyl sulfurofluoridate · ligand · 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
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 | 981 | 0.89 | 0.90 | 104 | empty |
| 2 | 409 | 0.84 | 0.92 | 49 | empty |
| 3 | 426 | 0.84 | 0.92 | 48 | empty |
| 4 | 198 | 0.51 | 0.77 | 29 | A7Z |
| 5 | 187 | 0.51 | 0.77 | 27 | A7Z |
Interfaces
12 interfaces between chains.
- C–E · 1033 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 1019 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1018 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 836 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 828 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 5UI4 · Structure of NME1 covalently conjugated to imidazole fluorosulfate · the same entry in another collection · chain F against F, TM-score 1.00
- P15531 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase a (P15531) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P15531
- Elsewhere: RCSB PDB 5UI4 · PDBe 5UI4 · UniProt P15531
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