MolNFT v1 · #177466 · protein + DNA

Human RAD51 post-synaptic complex

7EJE · DNA repair protein RAD51 homolog 1: “Human RAD51 post-synaptic complex”. Electron microscopy, 2 ligands (ANP, MG), 19 pockets (best druggability 0.79). MolNFT v1 #177466 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7EJE
Type: protein + DNA
Length: 951 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair protein RAD51 homolog 1; DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'); DNA…
UniProt: Q06609
Ligands: ANP, MG
Pockets: 19 · best druggability 0.79

Structure

electron microscopy · 3 distinct chains · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	DNA repair protein RAD51 homolog 1	protein	311	42% helix, 17% strand	Q06609
D	DNA (5'-D(PTPTPTPTPTPTPTPTP*T)-3')	dna	9	—	—
E	DNA (5'-D(PAPAPAPAPAPAPAPAP*A)-3')	dna	9	—	—

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 3 copies · chains A, B, C
MG · Magnesium ion · metal · 3 copies · chains A, B, C

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

Pockets

19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	139	0.79	0.96	23	empty
2	137	0.78	0.96	28	empty
3	259	0.74	0.88	39	MG, ANP
4	270	0.72	0.87	40	MG, ANP
5	514	0.69	0.79	45	empty

Interfaces

9 interfaces between chains.

B–C · 1953 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 1949 Å² buried · 30 hydrogen bonds · protein-protein
A–D · 583 Å² buried · 5 hydrogen bonds · protein-nucleic
B–D · 478 Å² buried · 6 hydrogen bonds · protein-nucleic
D–E · 361 Å² buried · 25 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

7EJE · human RAD51 post-synaptic complex · the same entry in another collection · chain D against D, 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 0.98

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 7EJE · PDBe 7EJE · UniProt Q06609

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