MolNFT v1 · #85988 · protein
Pseudomonas aeruginosa rmla in complex with allosteric inhibitor
4ASY · Glucose-1-phosphate thymidylyltransferase: “Pseudomonas aeruginosa rmla in complex with allosteric inhibitor”. X-ray diffraction, 2 ligands (N5Y, CL), 20 pockets (best druggability 0.82). MolNFT v1 #85988 on GenesisL1: 3D structure…
- PDB
- 4ASY
- Type
- protein
- Length
- 1,171 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-1-phosphate thymidylyltransferase
- EC
- 2.7.7.74
- UniProt
- G3XCK4
- Ligands
- N5Y, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.74) | protein | 293 | 34% helix, 24% strand | G3XCK4 |
| B | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.74) | protein | 292 | 37% helix, 24% strand | G3XCK4 |
Ligands and binding sites
- N5Y · N-(6-amino-1-benzyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-N-methylbenzamide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 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 | 146 | 0.82 | 0.98 | 24 | empty |
| 2 | 105 | 0.80 | 0.99 | 20 | empty |
| 3 | 486 | 0.73 | 0.82 | 40 | empty |
| 4 | 411 | 0.73 | 0.83 | 39 | empty |
| 5 | 336 | 0.71 | 0.84 | 28 | CL, N5Y |
Interfaces
6 interfaces between chains.
- C–D · 1971 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 1928 Ų buried · 48 hydrogen bonds · protein-protein
- B–D · 1362 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1258 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 27 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ASY · Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor · 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 G3XCK4
- Elsewhere: RCSB PDB 4ASY · PDBe 4ASY · UniProt G3XCK4
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