MolNFT v2 · #219026 · protein + DNA

Human RAD52 open ring - ssDNA complex

8RJW · DNA repair protein RAD52 homolog: “Human RAD52 open ring - ssDNA complex”. Electron microscopy at 2.3, 1 ligand (MG), 20 pockets (best druggability 0.76). MolNFT v2 #219026 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 8RJW
Type: protein + DNA
Length: 1,265 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.3
Source: Homo sapiens; SYNTHETIC CONSTRUCT
Molecule: DNA repair protein RAD52 homolog; ssDNA
UniProt: P43351
Ligands: MG
Pockets: 20 · best druggability 0.76

Structure

electron microscopy · resolution 2.3 · 10 distinct chains · 38% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA repair protein RAD52 homolog	protein	113	37% helix, 29% strand	P43351
B	DNA repair protein RAD52 homolog	protein	148	41% helix, 32% strand	P43351
C	DNA repair protein RAD52 homolog	protein	154	40% helix, 32% strand	P43351
D	DNA repair protein RAD52 homolog	protein	177	37% helix, 29% strand	P43351
E	DNA repair protein RAD52 homolog	protein	171	40% helix, 31% strand	P43351
F	DNA repair protein RAD52 homolog	protein	167	37% helix, 31% strand	P43351
G	DNA repair protein RAD52 homolog	protein	135	38% helix, 33% strand	P43351
H	DNA repair protein RAD52 homolog	protein	111	35% helix, 39% strand	P43351
I	DNA repair protein RAD52 homolog	protein	66	42% helix, 5% strand	P43351
J	ssDNA	dna	23	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 5 copies · chains B, C, D, E, F, J, G

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	252	0.76	0.89	39	empty
2	112	0.76	0.96	27	empty
3	218	0.75	0.90	40	empty
4	72	0.72	0.97	21	empty
5	67	0.70	0.96	15	empty

Interfaces

18 interfaces between chains.

C–D · 2471 Å² buried · 27 hydrogen bonds · protein-protein
D–E · 2346 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 2284 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 1525 Å² buried · 16 hydrogen bonds · protein-protein
F–G · 1488 Å² buried · 15 hydrogen bonds · protein-protein

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 8RJW · PDBe 8RJW · UniProt P43351

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.