MolNFT v1 · #143639 · protein
Mycobacterium tuberculosis rmla in complex with MG/DTTP
6B5K · Glucose-1-phosphate thymidylyltransferase: “Mycobacterium tuberculosis rmla in complex with MG/DTTP”. X-ray diffraction, 3 ligands (TTP, TYD, MG), 3 pockets (best druggability 0.76). MolNFT v1 #143639 on GenesisL1: 3D structure…
- PDB
- 6B5K
- Type
- protein
- Length
- 547 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-1-phosphate thymidylyltransferase
- EC
- 2.7.7.24
- UniProt
- P9WH13
- Ligands
- TTP, TYD, MG
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 277 | 40% helix, 21% strand | P9WH13 |
| B | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 270 | 41% helix, 20% strand | P9WH13 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains A, B
- TYD · Thymidine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.76 | 0.78 | 123 | TTP, MG, TYD |
| 2 | 618 | 0.68 | 0.77 | 65 | MG, TTP |
| 3 | 87 | 0.36 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 568 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6B5K · Mycobacterium tuberculosis RmlA in complex with Mg/dTTP · the same entry in another collection · chain A against A, TM-score 1.00
- P9WH13 · AlphaFold monomer V2.0 prediction for glucose-1-phosphate thymidylyltransferase (P9WH13) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P9WH13
- Elsewhere: RCSB PDB 6B5K · PDBe 6B5K · UniProt P9WH13
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