MolNFT v1 · #176668 · protein
Thil in complex with AMP-pnp
7DU3 · Thiamine-monophosphate kinase: “Thil in complex with AMP-pnp”. X-ray diffraction, 2 ligands (ANP, MG), 6 pockets (best druggability 0.65). MolNFT v1 #176668 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7DU3
- Type
- protein
- Length
- 638 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiamine-monophosphate kinase
- EC
- 2.7.4.16
- UniProt
- A0A232BM78
- Ligands
- ANP, MG
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiamine-monophosphate kinase (EC 2.7.4.16) | protein | 311 | 37% helix, 25% strand | A0A232BM78 |
| B | Thiamine-monophosphate kinase (EC 2.7.4.16) | protein | 327 | 35% helix, 24% strand | A0A232BM78 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.65 | 0.78 | 63 | empty |
| 2 | 279 | 0.55 | 0.76 | 44 | empty |
| 3 | 68 | 0.43 | 0.81 | 18 | empty |
| 4 | 71 | 0.42 | 0.80 | 19 | ANP |
| 5 | 64 | 0.30 | 0.75 | 22 | MG |
Interfaces
1 interface between chains.
- A–B · 628 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7DU3 · ThiL in complex with AMP-PNP · 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 A0A232BM78
- Elsewhere: RCSB PDB 7DU3 · PDBe 7DU3 · UniProt A0A232BM78
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