MolNFT v1 · #91275 · protein

Crystal structure of human PRS1 D52H mutant

4F8E · Ribose-phosphate pyrophosphokinase 1: “Crystal structure of human PRS1 D52H mutant”. X-ray diffraction, 2 ligands (MG, SO4), 5 pockets (best druggability 0.75). MolNFT v1 #91275 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4F8E
Type: protein
Length: 616 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribose-phosphate pyrophosphokinase 1
EC: 2.7.6.1
UniProt: P60891
Ligands: MG, SO4
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribose-phosphate pyrophosphokinase 1 (EC 2.7.6.1)	protein	308	37% helix, 24% strand	P60891
B	Ribose-phosphate pyrophosphokinase 1 (EC 2.7.6.1)	protein	308	35% helix, 26% strand	P60891

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 6 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1004	0.75	0.78	94	SO4
2	206	0.60	0.81	29	empty
3	153	0.57	0.82	30	empty
4	79	0.38	0.78	16	SO4
5	55	0.32	0.77	16	SO4

Interfaces

1 interface between chains.

A–B · 1486 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

4F8E · Crystal structure of human PRS1 D52H mutant · the same entry in another collection · chain A against A, TM-score 1.00
P60891 · AlphaFold monomer V2.0 prediction for ribose-phosphate pyrophosphokinase 1 (P60891) · a predicted model of the same protein · chain B 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 P60891
Elsewhere: RCSB PDB 4F8E · PDBe 4F8E · UniProt P60891

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