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Structure of ding in complex with ssdna

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

PDB: 6FWR
Type: protein + DNA
Length: 710 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-dependent DNA helicase ding; DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
UniProt: A0A2H4TNL0
Ligands: SF4
Pockets: 7 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 54% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP-dependent DNA helicase ding	protein	699	54% helix, 14% strand	A0A2H4TNL0
B	DNA (5'-D(TPTPTPTPTPTPTPTPTPTP*T)-3')	dna	11	—	—

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1053	0.86	0.87	98	empty
2	261	0.67	0.83	42	SF4
3	373	0.59	0.76	49	empty
4	139	0.47	0.78	23	empty
5	91	0.47	0.81	17	empty

Interfaces

1 interface between chains.

A–B · 1293 Å² buried · 29 hydrogen bonds · protein-nucleic

Compared structures

6FWR · Structure of DinG in complex with ssDNA · 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 A0A2H4TNL0
Elsewhere: RCSB PDB 6FWR · PDBe 6FWR · UniProt A0A2H4TNL0

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