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Crystal structure of the binary complex of RECD2 with DNA

Analyse Crystal structure of the binary complex of RECD2 with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GP8
Type: protein + DNA
Length: 559 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exodeoxyribonuclease V, subunit recd, putative…
UniProt: Q9RT63
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exodeoxyribonuclease V, subunit recd, putative	protein	551	45% helix, 16% strand	Q9RT63
X	5'-D(TPTPTPTPTPTTPTPTPTPTPTPTPT)-3'	dna	8	—	—

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	143	0.72	0.92	25	empty
2	264	0.68	0.84	35	empty
3	94	0.58	0.87	19	empty
4	368	0.58	0.75	44	empty
5	165	0.54	0.80	28	empty

Interfaces

1 interface between chains.

A–X · 1098 Å² buried · 25 hydrogen bonds · protein-nucleic

Compared structures

3GP8 · Crystal structure of the binary complex of RecD2 with DNA · the same entry in another collection · chain A against A, TM-score 1.00
Q9RT63 · AlphaFold monomer V2.0 prediction for ATP-dependent recd-like DNA helicase (Q9RT63) · 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 Q9RT63
Elsewhere: RCSB PDB 3GP8 · PDBe 3GP8 · UniProt Q9RT63

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