MolNFT v1 · #99309 · protein

Crystal structure of human PRS1 D65N mutant

4LZN · Ribose-phosphate pyrophosphokinase 1: “Crystal structure of human PRS1 D65N mutant”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.70). MolNFT v1 #99309 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4LZN
Type: protein
Length: 612 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: SO4
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Ribose-phosphate pyrophosphokinase 1 (EC 2.7.6.1)	protein	308	37% helix, 23% strand	P60891
A	Ribose-phosphate pyrophosphokinase 1 (EC 2.7.6.1)	protein	304	36% helix, 23% strand	P60891

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains B, A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	169	0.70	0.89	35	empty
2	144	0.66	0.88	28	empty
3	299	0.58	0.78	52	SO4
4	128	0.52	0.81	21	empty
5	231	0.49	0.75	32	SO4

Interfaces

1 interface between chains.

B–A · 2019 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

4LZN · Crystal structure of human PRS1 D65N mutant · the same entry in another collection · chain B against B, 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 4LZN · PDBe 4LZN · UniProt P60891

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