MolNFT v1 · #164605 · protein
Pseudomonas aeruginosa rmla in complex with allosteric inhibitor
6T38 · Glucose-1-phosphate thymidylyltransferase: “Pseudomonas aeruginosa rmla in complex with allosteric inhibitor”. X-ray diffraction, 3 ligands (MBK, CL, BR), 20 pockets (best druggability 0.76). MolNFT v1 #164605 on GenesisL1: 3D…
- PDB
- 6T38
- Type
- protein
- Length
- 1,132 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
- MBK, CL, BR
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 279 | 38% helix, 24% strand | Q9HU22 |
| B | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 289 | 38% helix, 23% strand | Q9HU22 |
| C | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 279 | 40% helix, 24% strand | Q9HU22 |
| D | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 285 | 39% helix, 24% strand | Q9HU22 |
Ligands and binding sites
- MBK · ~{N}-[6-(4-azanylbutylamino)-1-[(4-bromophenyl)methyl]-2,4-bis(oxidanylidene)pyrimidin-5-yl]-~{N}-methyl-benzenesulfonamide · ligand · 4 copies · chains A, D, B, C
- CL · Chloride ion · ion · 14 copies · chains A, D, B, C
- BR · Bromide ion · ion · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, D, B, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.76 | 0.97 | 17 | empty |
| 2 | 85 | 0.75 | 0.97 | 16 | empty |
| 3 | 332 | 0.71 | 0.84 | 29 | CL, MBK |
| 4 | 327 | 0.71 | 0.84 | 27 | MBK, CL |
| 5 | 337 | 0.70 | 0.83 | 28 | MBK, CL |
Interfaces
6 interfaces between chains.
- A–D · 1936 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 1929 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 902 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 902 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6T38 · 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 6T38 · PDBe 6T38 · UniProt Q9HU22
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