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Crystal structure of recombinational repair protein recr

Analyse Crystal structure of recombinational repair protein recr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1VDD
Type: protein
Length: 791 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Recombination protein recr
UniProt: Q9ZNA2
Ligands: ZN
Pockets: 7 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Recombination protein recr	protein	199	42% helix, 15% strand	Q9ZNA2
B, D	Recombination protein recr	protein	198	46% helix, 14% strand	Q9ZNA2
C	Recombination protein recr	protein	196	42% helix, 15% strand	Q9ZNA2

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
IMD · Imidazole · additive · 5 copies · chains A, C, B, 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	66	0.57	0.89	22	empty
2	149	0.44	0.76	23	empty
3	100	0.39	0.76	15	empty
4	97	0.37	0.75	18	empty
5	81	0.35	0.76	19	IMD

Interfaces

6 interfaces between chains.

A–C · 2580 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 2490 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 2485 Å² buried · 55 hydrogen bonds · protein-protein
C–D · 2390 Å² buried · 47 hydrogen bonds · protein-protein
A–D · 263 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1VDD · Crystal structure of recombinational repair protein RecR · the same entry in another collection · chain A against A, TM-score 1.00
Q9ZNA2 · AlphaFold monomer V2.0 prediction for recombination protein recr (Q9ZNA2) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q9ZNA2
Elsewhere: RCSB PDB 1VDD · PDBe 1VDD · UniProt Q9ZNA2

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