MolNFT v1 · #60275 · protein + DNA

Mechanism of homologous recombination from the reca-SSDNA/DSDNA structures

3CMW · DNA (5'- D(*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*…: “Mechanism of homologous recombination from the reca-SSDNA/DSDNA structures”. X-ray diffraction, 3 ligands (ALF, ADP, MG), 20 pockets (best druggability 0.83). MolNFT v1…

PDB: 3CMW
Type: protein + DNA
Length: 3,241 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DT)-3'); Protein reca
UniProt: P0A7G6
Ligands: ALF, ADP, MG
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, D	DNA (5'- D(DTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTP*DT)-3')	dna	12	—	—
A	Protein reca	protein	1609	40% helix, 26% strand	P0A7G6
C	Protein reca	protein	1608	40% helix, 26% strand	P0A7G6

Ligands and binding sites

ALF · Tetrafluoroaluminate ion · ligand · 10 copies · chains A, C
ADP · Adenosine-5'-diphosphate · ligand · 10 copies · chains A, C
MG · Magnesium ion · metal · 10 copies · chains A, C

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	925	0.83	0.85	95	MG, ALF, ADP
2	275	0.79	0.91	40	MG, ALF, ADP
3	627	0.79	0.84	76	MG, ALF, ADP
4	528	0.78	0.85	61	MG, ALF, ADP
5	559	0.78	0.84	67	MG, ALF, ADP

Interfaces

5 interfaces between chains.

A–C · 2514 Å² buried · 21 hydrogen bonds · protein-protein
B–A · 2266 Å² buried · 37 hydrogen bonds · protein-nucleic
D–C · 2215 Å² buried · 34 hydrogen bonds · protein-nucleic
D–A · 66 Å² buried · 0 hydrogen bonds · protein-nucleic
B–C · 49 Å² buried · 0 hydrogen bonds · protein-nucleic

Compared structures

3CMW · Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures · the same entry in another collection · chain C against C, TM-score 1.00
P0A7G6 · AlphaFold monomer V2.0 prediction for protein reca (P0A7G6) · a predicted model of the same protein · chain A against A, TM-score 0.21

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 P0A7G6
Elsewhere: RCSB PDB 3CMW · PDBe 3CMW · UniProt P0A7G6

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