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

Analyse Mechanism of homologous recombination from the reca-SSDNA/DSDNA structures in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CMX
Type: protein + DNA
Length: 3,253 residues
Chains: 6
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'); DNA…
UniProt: P0A7G6
Ligands: ALF, ADP, MG
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, E	DNA (5'- D(DTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTP*DT)-3')	dna	13	—	—
C	DNA (5'-D(DAPDAPDAPDAPDAPDAPDAPDAPDAPDAPDAPDA)- 3')	dna	10	—	—
F	DNA (5'-D(DAPDAPDAPDAPDAPDAPDAPDAPDAPDAPDAPDA)- 3')	dna	11	—	—
A, D	Protein reca	protein	1603	39% helix, 25% strand	P0A7G6

Ligands and binding sites

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

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	838	0.81	0.84	104	MG, ALF, ADP
2	440	0.79	0.87	64	MG, ALF, ADP
3	434	0.79	0.87	62	ALF, ADP
4	673	0.78	0.83	78	MG, ALF, ADP
5	1026	0.78	0.80	93	empty

Interfaces

9 interfaces between chains.

A–D · 2539 Å² buried · 20 hydrogen bonds · protein-protein
B–A · 2287 Å² buried · 25 hydrogen bonds · protein-nucleic
E–D · 2202 Å² buried · 25 hydrogen bonds · protein-nucleic
F–D · 1012 Å² buried · 7 hydrogen bonds · protein-nucleic
C–A · 917 Å² buried · 4 hydrogen bonds · protein-nucleic

Compared structures

3CMX · Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures · the same entry in another collection · chain E against E, 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 3CMX · PDBe 3CMX · UniProt P0A7G6

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