MolNFT v1 · #86392 · protein
Pseudomonas aeruginosa rmla in complex with allosteric inhibitor
4B5B · Glucose-1-phosphate thymidylyltransferase: “Pseudomonas aeruginosa rmla in complex with allosteric inhibitor”. X-ray diffraction, 2 ligands (BBE, CL), 20 pockets (best druggability 0.81). MolNFT v1 #86392 on GenesisL1: 3D structure…
- PDB
- 4B5B
- Type
- protein
- Length
- 1,170 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
- Q9HU22
- Ligands
- BBE, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.74) | protein | 293 | 37% helix, 24% strand | Q9HU22 |
| C | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.74) | protein | 291 | 38% helix, 23% strand | Q9HU22 |
Ligands and binding sites
- BBE · N-(6-amino-1-benzyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-N,3-dimethylbenzenesulfonamide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 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 | 116 | 0.81 | 0.99 | 19 | empty |
| 2 | 87 | 0.78 | 0.99 | 17 | empty |
| 3 | 429 | 0.74 | 0.84 | 43 | empty |
| 4 | 423 | 0.73 | 0.83 | 40 | empty |
| 5 | 403 | 0.70 | 0.82 | 42 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1396 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1343 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 376 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 301 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 121 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4B5B · 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 4B5B · PDBe 4B5B · UniProt Q9HU22
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