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Crystal structure of PprA A139R mutant

Analyse Crystal structure of PprA A139R mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6A29
Type: protein
Length: 2,203 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.399
Source: Deinococcus radiodurans R1
Molecule: DNA repair protein PprA
UniProt: O32504
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · resolution 2.399 · 2 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F, G, H	DNA repair protein PprA	protein	275	48% helix, 17% strand	O32504
E	DNA repair protein PprA	protein	278	46% helix, 16% strand	O32504

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1048	0.76	0.79	87	empty
2	897	0.75	0.79	86	empty
3	1008	0.74	0.77	67	empty
4	362	0.74	0.85	52	empty
5	93	0.73	0.96	26	empty

Interfaces

11 interfaces between chains.

B–E · 1821 Å² buried · 18 hydrogen bonds · protein-protein
D–G · 1758 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1038 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 1025 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 999 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6A29 · Crystal structure of ppra A139R mutant · the same entry in another collection · chain H against H, TM-score 1.00
O32504 · AlphaFold monomer V2.0 prediction for DNA repair protein ppra (O32504) · a predicted model of the same protein · chain E against A, TM-score 0.92

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 O32504
Elsewhere: RCSB PDB 6A29 · PDBe 6A29 · UniProt O32504

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