MolNFT v1 · #100870 · protein

Prcb from geobacillus kaustophilus, apo structure

4NAF · Heptaprenylglyceryl phosphate synthase: “Prcb from geobacillus kaustophilus, apo structure”. X-ray diffraction, 2 pockets (best druggability 0.75). MolNFT v1 #100870 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4NAF
Type: protein
Length: 445 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heptaprenylglyceryl phosphate synthase
EC: 2.5.1.-
UniProt: Q5L3C1
Pockets: 2 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heptaprenylglyceryl phosphate synthase (EC 2.5.1.-)	protein	223	44% helix, 20% strand	Q5L3C1
B	Heptaprenylglyceryl phosphate synthase	protein	222	42% helix, 20% strand	Q5L3C1

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	486	0.75	0.83	59	empty
2	468	0.73	0.82	57	empty

Interfaces

1 interface between chains.

A–B · 1490 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4NAF · PrcB from Geobacillus kaustophilus, apo structure · the same entry in another collection · chain A against A, TM-score 1.00
Q5L3C1 · AlphaFold monomer V2.0 prediction for heptaprenylglyceryl phosphate synthase (Q5L3C1) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q5L3C1
Elsewhere: RCSB PDB 4NAF · PDBe 4NAF · UniProt Q5L3C1

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