MolNFT v1 · #120467 · protein + DNA

Human RAD51 presynaptic complex

5H1B · DNA repair protein RAD51 homolog 1: “Human RAD51 presynaptic complex”. Electron microscopy, 2 ligands (ANP, MG), 18 pockets (best druggability 0.78). MolNFT v1 #120467 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5H1B
Type: protein + DNA
Length: 933 residues
Chains: 4
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')
UniProt: Q06609
Ligands: ANP, MG
Pockets: 18 · best druggability 0.78

Structure

electron microscopy · 2 distinct chains · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	DNA repair protein RAD51 homolog 1	protein	308	44% helix, 18% strand	Q06609
D	DNA (5'-D(PTPTPTPTPTPTPTPTP*T)-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

18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	135	0.78	0.96	22	empty
2	200	0.76	0.91	37	ANP, MG
3	189	0.75	0.91	38	ANP, MG
4	108	0.74	0.95	23	empty
5	548	0.74	0.82	64	empty

Interfaces

5 interfaces between chains.

B–C · 1904 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 1887 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 667 Å² buried · 12 hydrogen bonds · protein-nucleic
C–D · 561 Å² buried · 9 hydrogen bonds · protein-nucleic
A–D · 538 Å² buried · 9 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 3 covalent (covalent ligand).

Compared structures

5H1B · Human RAD51 presynaptic complex · the same entry in another collection · chain A against A, 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 5H1B · PDBe 5H1B · UniProt Q06609

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