MolNFT v1 · #177465 · protein + DNA

Human RAD51 presynaptic complex

7EJC · DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'): “Human RAD51 presynaptic complex”. Electron microscopy, 3 ligands (J46, ANP, MG), 15 pockets (best druggability 0.83). MolNFT v1 #177465 on GenesisL1: 3D structure, binding sites and…

PDB: 7EJC
Type: protein + DNA
Length: 939 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'); DNA repair protein RAD51 homolog 1
UniProt: Q06609
Ligands: J46, ANP, MG
Pockets: 15 · best druggability 0.83

Structure

electron microscopy · 2 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	DNA (5'-D(PTPTPTPTPTPTPTPTP*T)-3')	dna	9	—	—
A, C, B	DNA repair protein RAD51 homolog 1	protein	310	41% helix, 18% strand	Q06609

Ligands and binding sites

J46 · 4-bromanyl-N-(4-bromophenyl)-3-[(phenylmethyl) sulfamoyl]benzamide · ligand · 3 copies · chains A, C, B
ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 3 copies · chains C, B, A
MG · Magnesium ion · metal · 3 copies · chains A, C, B

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

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	378	0.83	0.92	48	ANP, MG
2	350	0.82	0.92	50	ANP
3	341	0.67	0.81	35	J46
4	429	0.65	0.78	40	empty
5	267	0.64	0.81	23	J46

Interfaces

5 interfaces between chains.

C–B · 1885 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1879 Å² buried · 18 hydrogen bonds · protein-protein
G–B · 646 Å² buried · 8 hydrogen bonds · protein-nucleic
G–C · 537 Å² buried · 7 hydrogen bonds · protein-nucleic
G–A · 525 Å² buried · 7 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

7EJC · human RAD51 presynaptic complex · the same entry in another collection · chain G against G, TM-score 1.00
Q06609 · AlphaFold monomer V2.0 prediction for DNA repair protein RAD51 homolog 1 (Q06609) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q06609
Elsewhere: RCSB PDB 7EJC · PDBe 7EJC · UniProt Q06609

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