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Crystal structure of the dnac-ssdna complex

Analyse Crystal structure of the dnac-ssdna complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VYE
Type: protein + DNA
Length: 813 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Replicative DNA helicase; 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP)-3'
EC: 3.6.1.-
UniProt: Q5KU75
Pockets: 15 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 56% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Replicative DNA helicase (EC 3.6.1.-)	protein	424	55% helix, 13% strand	Q5KU75
B	Replicative DNA helicase (EC 3.6.1.-)	protein	380	57% helix, 9% strand	Q5KU75
C	5'-D(TPTPTPTPTPTPTPTP*TP)-3'	dna	9	—	—

Pockets

15 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	792	0.77	0.82	65	empty
2	687	0.73	0.79	72	empty
3	294	0.64	0.81	34	empty
4	192	0.63	0.83	35	empty
5	210	0.56	0.79	29	empty

Interfaces

3 interfaces between chains.

A–B · 1628 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 749 Å² buried · 24 hydrogen bonds · protein-nucleic
A–C · 184 Å² buried · 3 hydrogen bonds · protein-nucleic

Compared structures

2VYE · Crystal Structure of the DnaC-ssDNA complex · the same entry in another collection · chain A against A, TM-score 1.00

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 Q5KU75
Elsewhere: RCSB PDB 2VYE · PDBe 2VYE · UniProt Q5KU75

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