MolNFT v1 · #35370 · protein
E. COLI undecaprenyl pyrophosphate synthase in complex with bph-675
2E9C · Undecaprenyl pyrophosphate synthetase: “E. COLI undecaprenyl pyrophosphate synthase in complex with bph-675”. X-ray diffraction, 1 ligand (B75), 6 pockets (best druggability 0.71). MolNFT v1 #35370 on GenesisL1: 3D structure…
- PDB
- 2E9C
- Type
- protein
- Length
- 421 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
- B75
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) | protein | 208 | 46% helix, 14% strand | P60472 |
| B | Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) | protein | 213 | 49% helix, 14% strand | P60472 |
Ligands and binding sites
- B75 · 1-hydroxy-2-[3'-(naphthalene-2-sulfonylamino)-biphenyl-3-yl]ethylidene-1,1-bisphosphonic acid · ligand · 4 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 | 635 | 0.71 | 0.78 | 46 | B75 |
| 2 | 304 | 0.56 | 0.76 | 43 | B75 |
| 3 | 60 | 0.40 | 0.81 | 18 | empty |
| 4 | 58 | 0.38 | 0.80 | 17 | empty |
| 5 | 94 | 0.34 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1913 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 2E9C · E. coli undecaprenyl pyrophosphate synthase in complex with BPH-675 · 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 2E9C · PDBe 2E9C · UniProt P60472
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