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Crystal structure of glucose-1-phosphate thymidylyltransferase, rmla, complex with dtdp
Analyse Crystal structure of glucose-1-phosphate thymidylyltransferase, rmla, complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LVW
- Type
- protein
- Length
- 1,170 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-1-phosphate thymidylyltransferase
- EC
- 2.7.7.24
- UniProt
- O27819
- Ligands
- TYD, CL, SO4
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 295 | 36% helix, 21% strand | O27819 |
| B | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 292 | 36% helix, 21% strand | O27819 |
| C | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 292 | 36% helix, 21% strand | O27819 |
| D | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 291 | 36% helix, 21% strand | O27819 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 8 copies · chains A, C, B, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, D
- GOL · Glycerol · additive · 11 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.76 | 0.99 | 18 | empty |
| 2 | 64 | 0.73 | 0.98 | 17 | empty |
| 3 | 220 | 0.70 | 0.87 | 32 | empty |
| 4 | 615 | 0.65 | 0.75 | 73 | CL, TYD, GOL |
| 5 | 503 | 0.64 | 0.76 | 47 | CL, TYD |
Interfaces
5 interfaces between chains.
- A–C · 2159 Ų buried · 56 hydrogen bonds · protein-protein
- B–D · 2061 Ų buried · 51 hydrogen bonds · protein-protein
- B–C · 1504 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1496 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1LVW · Crystal structure of glucose-1-phosphate thymidylyltransferase, RmlA, complex with dTDP · 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 O27819
- Elsewhere: RCSB PDB 1LVW · PDBe 1LVW · UniProt O27819
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