MolNFT v1 · #7265 · protein
The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (rmla). tdp-glucose complex.
1G1L: “The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase…”. X-ray diffraction, 2 ligands (DAU, SO4), 20 pockets (best druggability 0.78). MolNFT v1 #7265 on GenesisL1: 3D structure…
- PDB
- 1G1L
- Type
- protein
- Length
- 2,338 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
- Q9HU22
- Ligands
- DAU, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, G, H | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 292 | 39% helix, 23% strand | Q9HU22 |
| B, F | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 293 | 40% helix, 23% strand | Q9HU22 |
Ligands and binding sites
- DAU · 2'deoxy-thymidine-5'-diphospho-alpha-D-glucose · ligand · 16 copies · chains A, C, B, D, E, H, F, G
- SO4 · Sulfate ion · ion · 23 copies · chains A, B, C, D, E, F, H, G
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.78 | 0.99 | 16 | empty |
| 2 | 85 | 0.77 | 0.98 | 16 | empty |
| 3 | 78 | 0.77 | 0.99 | 18 | empty |
| 4 | 599 | 0.76 | 0.83 | 63 | DAU |
| 5 | 66 | 0.75 | 0.99 | 14 | empty |
Interfaces
13 interfaces between chains.
- F–G · 1991 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 1970 Ų buried · 50 hydrogen bonds · protein-protein
- E–H · 1969 Ų buried · 42 hydrogen bonds · protein-protein
- B–D · 1966 Ų buried · 47 hydrogen bonds · protein-protein
- G–H · 1348 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1G1L · The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate… · 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 Q9HU22
- Elsewhere: RCSB PDB 1G1L · PDBe 1G1L · UniProt Q9HU22
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