MolNFT v1 · #86315 · protein
Pseudomonas aeruginosa rmla in complex with allosteric inhibitor
4B2W · Glucose-1-phosphate thymidylyltransferase: “Pseudomonas aeruginosa rmla in complex with allosteric inhibitor”. X-ray diffraction, 2 ligands (BZ0, CL), 20 pockets (best druggability 0.81). MolNFT v1 #86315 on GenesisL1: 3D structure…
- PDB
- 4B2W
- Type
- protein
- Length
- 1,165 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
- BZ0, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.74) | protein | 297 | 37% helix, 22% strand | G3XCK4 |
| B, D | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.74) | protein | 290 | 38% helix, 23% strand | G3XCK4 |
| C | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.74) | protein | 288 | 39% helix, 23% strand | G3XCK4 |
Ligands and binding sites
- BZ0 · N-(6-amino-1-benzyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)benzamide · 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
- GOL · Glycerol · additive · chains 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 | 137 | 0.81 | 0.98 | 22 | empty |
| 2 | 89 | 0.79 | 0.99 | 16 | empty |
| 3 | 1007 | 0.78 | 0.80 | 122 | empty |
| 4 | 485 | 0.74 | 0.83 | 42 | empty |
| 5 | 505 | 0.73 | 0.82 | 51 | GOL |
Interfaces
5 interfaces between chains.
- A–D · 1422 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1347 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 534 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 389 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 148 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4B2W · 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 4B2W · PDBe 4B2W · UniProt G3XCK4
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