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
- 6TQG
- Type
- protein
- Length
- 1,069 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
- G3XCK4
- Ligands
- NVQ, CL
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 278 | 36% helix, 24% strand | G3XCK4 |
| B | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 271 | 39% helix, 25% strand | G3XCK4 |
| C | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 259 | 37% helix, 26% strand | G3XCK4 |
| D | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 261 | 39% helix, 25% strand | G3XCK4 |
Ligands and binding sites
- NVQ · ~{N}-[1-[(4-bromophenyl)methyl]-6-[3-(methylamino) propylamino]-2,4-bis(oxidanylidene)pyrimidin-5-yl]-~{N}-methyl-benzenesulfonamide · ligand · 4 copies · chains A, C, B, D
- CL · Chloride ion · ion · 8 copies · chains A, C, B, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, C, B, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.72 | 0.84 | 29 | NVQ, CL |
| 2 | 321 | 0.72 | 0.85 | 27 | CL, NVQ |
| 3 | 332 | 0.71 | 0.84 | 32 | NVQ, CL |
| 4 | 67 | 0.70 | 0.96 | 16 | empty |
| 5 | 314 | 0.69 | 0.83 | 28 | CL, NVQ |
Interfaces
6 interfaces between chains.
- A–C · 1921 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 1910 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 871 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 567 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6TQG · 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 6TQG · PDBe 6TQG · UniProt G3XCK4
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