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
- 5FU8
- Type
- protein
- Length
- 1,177 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
- DH5, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 297 | 37% helix, 22% strand | Q9HU22 |
| B | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 293 | 36% helix, 23% strand | Q9HU22 |
| C | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 295 | 39% helix, 22% strand | Q9HU22 |
| D | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 292 | 38% helix, 24% strand | Q9HU22 |
Ligands and binding sites
- DH5 · N-(6-amino-1-(4-bromo-3-methylbenzyl)-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-N-methylbenzenesulfonamide · 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.80 | 0.99 | 16 | empty |
| 2 | 84 | 0.77 | 0.98 | 16 | empty |
| 3 | 401 | 0.73 | 0.84 | 39 | empty |
| 4 | 479 | 0.73 | 0.82 | 46 | empty |
| 5 | 379 | 0.71 | 0.83 | 40 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1416 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1352 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 488 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 383 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 275 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5FU8 · 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 5FU8 · PDBe 5FU8 · UniProt Q9HU22
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