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
- 6T37
- Type
- protein
- Length
- 1,144 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
- M9Z, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 289 | 37% helix, 23% strand | G3XCK4 |
| B | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 289 | 37% helix, 22% strand | G3XCK4 |
| C | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 280 | 39% helix, 24% strand | G3XCK4 |
| D | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 286 | 40% helix, 23% strand | G3XCK4 |
Ligands and binding sites
- M9Z · ~{N}-[6-[3-[4-(aminomethyl)-1,2,3-triazol-1-yl]propylamino]-2,4-bis(oxidanylidene)-1-(phenylmethyl)pyrimidin-5-yl]-~{N}-methyl-benzenesulfonamide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, C
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 | 101 | 0.79 | 0.98 | 17 | empty |
| 2 | 75 | 0.76 | 0.98 | 14 | empty |
| 3 | 1189 | 0.74 | 0.77 | 110 | CL |
| 4 | 428 | 0.69 | 0.80 | 47 | empty |
| 5 | 424 | 0.67 | 0.80 | 42 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1399 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1170 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 380 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 328 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 172 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6T37 · 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 6T37 · PDBe 6T37 · UniProt G3XCK4
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