MolNFT v1 · #78691 · protein
Crystal structure of E. COLI undecaprenyl pyrophosphate synthase in complex with bph-1299
3SGT: “Crystal structure of E. COLI undecaprenyl pyrophosphate synthase in complex with bph-1299”. X-ray diffraction, 1 ligand (P09), 6 pockets (best druggability 0.77). MolNFT v1 #78691 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3SGT
- Type
- protein
- Length
- 431 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Undecaprenyl pyrophosphate synthase
- EC
- 2.5.1.31
- UniProt
- P60473
- Ligands
- P09
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 225 | 50% helix, 14% strand | P60473 |
| A | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 206 | 48% helix, 14% strand | P60473 |
Ligands and binding sites
- P09 · 2-{[4-(3,4-dimethylphenoxy)phenyl]carbamoyl}benzoic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.77 | 0.84 | 56 | P09 |
| 2 | 336 | 0.64 | 0.79 | 36 | empty |
| 3 | 65 | 0.39 | 0.80 | 22 | empty |
| 4 | 67 | 0.39 | 0.79 | 19 | empty |
| 5 | 109 | 0.37 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- B–A · 1937 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 3SGT · Crystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1299 · the same entry in another collection · chain B against B, TM-score 1.00
- P60473 · AlphaFold monomer V2.0 prediction for DITRANS,POLYCIS-undecaprenyl- diphosphate synthase… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P60473
- Elsewhere: RCSB PDB 3SGT · PDBe 3SGT · UniProt P60473
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