Research workbench
Pseudomonas aeruginosa rmla in complex with allosteric inhibitor
Analyse Pseudomonas aeruginosa rmla in complex with allosteric inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B3U
- Type
- protein
- Length
- 1,183 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
- NWL, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 299 | 36% helix, 21% strand | Q9HU22 |
| B, D | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 293 | 34% helix, 24% strand | Q9HU22 |
| C | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 298 | 38% helix, 22% strand | Q9HU22 |
Ligands and binding sites
- NWL · 6-amino-1-benzyl-5-(ethylamino)pyrimidine-2,4(1H,3H)-dione · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.80 | 0.98 | 24 | empty |
| 2 | 87 | 0.78 | 0.99 | 17 | GOL |
| 3 | 750 | 0.75 | 0.80 | 83 | empty |
| 4 | 462 | 0.73 | 0.83 | 41 | empty |
| 5 | 427 | 0.73 | 0.83 | 42 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1438 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1298 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 613 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 386 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 348 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4B3U · 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 Q9HU22
- Elsewhere: RCSB PDB 4B3U · PDBe 4B3U · UniProt Q9HU22
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