MolNFT v1 · #139843 · protein + DNA

Structure of a ssdna bound to the inner DNA binding site of RAD52

5XRZ · DNA repair protein RAD52 homolog: “Structure of a ssdna bound to the inner DNA binding site of RAD52”. X-ray diffraction, 1 ligand (K), 20 pockets (best druggability 0.71). MolNFT v1 #139843 on GenesisL1: 3D structure, binding sites…

PDB: 5XRZ
Type: protein + DNA
Length: 2,064 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair protein RAD52 homolog; Ssdna (40-mer)
UniProt: P43351
Ligands: K
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K	DNA repair protein RAD52 homolog	protein	184	37% helix, 28% strand	P43351
L	Ssdna (40-mer)	dna	40	—	—

Ligands and binding sites

K · Potassium ion · metal · 10 copies · chains A, B, L, C, D, E, F, G, H, I, J, K

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	768	0.71	0.77	68	K
2	313	0.67	0.82	48	empty
3	118	0.63	0.87	17	empty
4	128	0.63	0.87	19	empty
5	116	0.63	0.87	18	empty

Interfaces

33 interfaces between chains.

B–C · 2648 Å² buried · 43 hydrogen bonds · protein-protein
D–E · 2640 Å² buried · 45 hydrogen bonds · protein-protein
I–J · 2636 Å² buried · 44 hydrogen bonds · protein-protein
F–G · 2626 Å² buried · 41 hydrogen bonds · protein-protein
E–F · 2625 Å² buried · 44 hydrogen bonds · protein-protein

Compared structures

5XRZ · Structure of a ssDNA bound to the inner DNA binding site of RAD52 · the same entry in another collection · chain L against L, TM-score 1.00

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 P43351
Elsewhere: RCSB PDB 5XRZ · PDBe 5XRZ · UniProt P43351

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