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
- 4B42
- Type
- protein
- Length
- 1,168 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
- 942, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.74) | protein | 293 | 37% helix, 23% strand | G3XCK4 |
| B | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.74) | protein | 291 | 37% helix, 24% strand | G3XCK4 |
| D | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.74) | protein | 291 | 37% helix, 24% strand | G3XCK4 |
Ligands and binding sites
- 942 · N-[6-azanyl-1-butyl-2,4-bis(oxidanylidene)pyrimidin-5-yl]-N-methyl-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
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 | 115 | 0.80 | 0.98 | 24 | empty |
| 2 | 111 | 0.80 | 0.98 | 19 | empty |
| 3 | 844 | 0.76 | 0.80 | 104 | empty |
| 4 | 456 | 0.74 | 0.83 | 43 | empty |
| 5 | 461 | 0.74 | 0.83 | 44 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1415 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1310 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 379 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 256 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 146 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4B42 · 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 4B42 · PDBe 4B42 · UniProt G3XCK4
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