MolNFT v1 · #35371 · protein
E. COLI undecaprenyl pyrophosphate synthase in complex with bph-676
2E9D · Undecaprenyl pyrophosphate synthetase: “E. COLI undecaprenyl pyrophosphate synthase in complex with bph-676”. X-ray diffraction, 1 ligand (B76), 5 pockets (best druggability 0.72). MolNFT v1 #35371 on GenesisL1: 3D structure…
- PDB
- 2E9D
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Undecaprenyl pyrophosphate synthetase
- EC
- 2.5.1.31
- UniProt
- P60472
- Ligands
- B76
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) | protein | 218 | 50% helix, 12% strand | P60472 |
| B | Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) | protein | 217 | 49% helix, 14% strand | P60472 |
Ligands and binding sites
- B76 · [1-hydroxy-2-(1,1':3',1''-terphenyl-3-yloxy)ethane-1,1-diyl]bis(phosphonic acid) · ligand · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.72 | 0.78 | 50 | B76 |
| 2 | 645 | 0.69 | 0.77 | 44 | B76 |
| 3 | 65 | 0.41 | 0.81 | 17 | empty |
| 4 | 101 | 0.35 | 0.74 | 20 | empty |
| 5 | 84 | 0.32 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1977 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 2E9D · E. coli undecaprenyl pyrophosphate synthase in complex with BPH-676 · 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 0.95
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 2E9D · PDBe 2E9D · UniProt P60472
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