MolNFT v1 · #76110 · protein

Structure of undecaprenyl diphosphate synthase

3QAS · Undecaprenyl pyrophosphate synthase: “Structure of undecaprenyl diphosphate synthase”. X-ray diffraction, 7 pockets (best druggability 0.65). MolNFT v1 #76110 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3QAS
Type: protein
Length: 434 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
Pockets: 7 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Undecaprenyl pyrophosphate synthase (EC 2.5.1.31)	protein	211	46% helix, 13% strand	P60472
A	Undecaprenyl pyrophosphate synthase (EC 2.5.1.31)	protein	223	50% helix, 13% strand	P60472

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	309	0.65	0.81	33	empty
2	208	0.63	0.83	37	empty
3	291	0.55	0.76	30	empty
4	78	0.43	0.80	22	empty
5	141	0.42	0.75	24	empty

Interfaces

1 interface between chains.

B–A · 1941 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

3QAS · Structure of Undecaprenyl Diphosphate synthase · the same entry in another collection · chain B against B, 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 3QAS · PDBe 3QAS · UniProt P60472

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