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Crystal structure of the purr complexed with cprpp

Analyse Crystal structure of the purr complexed with cprpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1P4A
Type: protein
Length: 1,074 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pur operon repressor
UniProt: P37551
Ligands: PCP
Pockets: 7 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pur operon repressor	protein	269	39% helix, 26% strand	P37551
B, D	Pur operon repressor	protein	268	39% helix, 31% strand	P37551
C	Pur operon repressor	protein	269	39% helix, 26% strand	P37551

Ligands and binding sites

PCP · 1-alpha-pyrophosphoryl-2-alpha,3-alpha-dihydroxy-4-beta-cyclopentane-methanol-5-phosphate · ligand · 4 copies · chains A, B, C, D

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

Pockets

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	679	0.80	0.85	57	empty
2	695	0.80	0.84	64	empty
3	1163	0.77	0.79	109	PCP
4	615	0.72	0.80	63	PCP
5	505	0.72	0.81	56	PCP

Interfaces

3 interfaces between chains.

A–B · 1872 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 1837 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 478 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1P4A · Crystal Structure of the PurR complexed with cPRPP · the same entry in another collection · chain A against A, TM-score 1.00
P37551 · AlphaFold monomer V2.0 prediction for pur operon repressor (P37551) · 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 P37551
Elsewhere: RCSB PDB 1P4A · PDBe 1P4A · UniProt P37551

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