MolNFT v1 · #93441 · protein
Structure of E. COLI undecaprenyl diphosphate synthase in complex with bph-1408
4H2M · Undecaprenyl pyrophosphate synthase: “Structure of E. COLI undecaprenyl diphosphate synthase in complex with bph-1408”. X-ray diffraction, 1 ligand (0YV), 6 pockets (best druggability 0.61). MolNFT v1 #93441 on GenesisL1: 3D…
- PDB
- 4H2M
- Type
- protein
- Length
- 427 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
- 0YV
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 214 | 48% helix, 14% strand | P60472 |
| B | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 213 | 49% helix, 14% strand | P60472 |
Ligands and binding sites
- 0YV · 2,2'-{benzene-1,3-diylbis[ethyne-2,1-diyl(5-bromobenzene-3,1-diyl)]}diethanamine · 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 | 272 | 0.61 | 0.79 | 36 | 0YV |
| 2 | 250 | 0.61 | 0.80 | 35 | 0YV |
| 3 | 70 | 0.41 | 0.80 | 21 | empty |
| 4 | 61 | 0.38 | 0.80 | 17 | empty |
| 5 | 97 | 0.33 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1864 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 4H2M · Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-1408 · 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 0.96
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 4H2M · PDBe 4H2M · UniProt P60472
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