Research workbench
Mycobacterium tuberculosis rmla in complex with dtdp-glucose
Analyse Mycobacterium tuberculosis rmla in complex with dtdp-glucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B5E
- Type
- protein
- Length
- 2,274 residues
- Chains
- 8
- 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
- DAU, TYD, MG, NA, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 283 | 40% helix, 22% strand | P9WH13 |
| B, C, D, E | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 286 | 38% helix, 21% strand | P9WH13 |
| F, G | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 284 | 38% helix, 21% strand | P9WH13 |
| H | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 279 | 39% helix, 20% strand | P9WH13 |
Ligands and binding sites
- DAU · 2'deoxy-thymidine-5'-diphospho-alpha-D-glucose · ligand · 10 copies · chains A, B, C, D, E, F, G, H
- TYD · Thymidine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, G, H
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D, E, F, G, H
- NA · Sodium ion · metal · 2 copies · chains B, C
- CL · Chloride ion · ion · 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
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.79 | 0.84 | 85 | TYD, DAU, MG |
| 2 | 424 | 0.78 | 0.87 | 30 | empty |
| 3 | 1043 | 0.77 | 0.79 | 99 | DAU, MG |
| 4 | 378 | 0.76 | 0.87 | 30 | empty |
| 5 | 588 | 0.76 | 0.83 | 69 | DAU, MG |
Interfaces
11 interfaces between chains.
- D–G · 1658 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1633 Ų buried · 20 hydrogen bonds · protein-protein
- F–H · 1622 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 1592 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 726 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6B5E · Mycobacterium tuberculosis RmlA in complex with dTDP-glucose · the same entry in another collection · chain H against H, TM-score 1.00
- P9WH13 · AlphaFold monomer V2.0 prediction for glucose-1-phosphate thymidylyltransferase (P9WH13) · a predicted model of the same protein · chain H 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 P9WH13
- Elsewhere: RCSB PDB 6B5E · PDBe 6B5E · UniProt P9WH13
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