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The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (rmla). tdp-L-rhamnose complex.
Analyse The structural basis of the catalytic mechanism and regulation of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G3L
- Type
- protein
- Length
- 1,169 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
- Q9HU22
- Ligands
- TRH, SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 292 | 36% helix, 23% strand | Q9HU22 |
| D | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 293 | 37% helix, 23% strand | Q9HU22 |
Ligands and binding sites
- TRH · 2'-deoxy-thymidine-beta-L-rhamnose · ligand · 8 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.76 | 0.98 | 17 | empty |
| 2 | 537 | 0.75 | 0.83 | 55 | TRH |
| 3 | 67 | 0.75 | 0.99 | 16 | empty |
| 4 | 441 | 0.74 | 0.84 | 40 | TRH |
| 5 | 465 | 0.74 | 0.83 | 44 | TRH |
Interfaces
6 interfaces between chains.
- A–C · 1956 Ų buried · 42 hydrogen bonds · protein-protein
- B–D · 1934 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 1492 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1471 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 35 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1G3L · 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 1G3L · PDBe 1G3L · UniProt Q9HU22
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