MolNFT v1 · #93465 · protein
Structure of E. COLI undecaprenyl diphosphate synthase in complex with bph-1330
4H3A · Undecaprenyl pyrophosphate synthase: “Structure of E. COLI undecaprenyl diphosphate synthase in complex with bph-1330”. X-ray diffraction, 1 ligand (0YY), 6 pockets (best druggability 0.65). MolNFT v1 #93465 on GenesisL1: 3D…
- PDB
- 4H3A
- Type
- protein
- Length
- 415 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
- P60472
- Ligands
- 0YY
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 208 | 44% helix, 14% strand | P60472 |
| B | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 207 | 49% helix, 14% strand | P60472 |
Ligands and binding sites
- 0YY · (2Z)-2-hydroxy-4-[4-(octyloxy)phenyl]-4-oxobut-2-enoic acid · ligand · 2 copies · chains A, 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 | 329 | 0.65 | 0.80 | 37 | 0YY |
| 2 | 266 | 0.61 | 0.80 | 31 | 0YY |
| 3 | 54 | 0.39 | 0.81 | 16 | empty |
| 4 | 109 | 0.36 | 0.74 | 23 | empty |
| 5 | 59 | 0.36 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1834 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4H3A · Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-1330 · the same entry in another collection · chain A against A, TM-score 1.00
- P60472 · AlphaFold monomer V2.0 prediction for DITRANS,POLYCIS-undecaprenyl- diphosphate synthase… · a predicted model of the same protein · chain B 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 P60472
- Elsewhere: RCSB PDB 4H3A · PDBe 4H3A · UniProt P60472
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