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Crystal structure of an xpd DNA complex

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

PDB: 4A15
Type: protein + DNA
Length: 600 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-dependent DNA helicase TA0057; 5'-D(*DTP*AP*CP*GP)-3'
EC: 3.6.4.12
UniProt: Q9HM14
Ligands: SF4, CA, SO4
Pockets: 4 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 56% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP-dependent DNA helicase TA0057 (EC 3.6.4.12)	protein	596	56% helix, 15% strand	Q9HM14
E	5'-D(DTPAPCPGP)-3'	dna	4	—	—

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains A
CA · Calcium ion · metal · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A

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

Pockets

4 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	1040	0.74	0.77	75	SO4
2	151	0.71	0.90	34	empty
3	318	0.56	0.75	53	SO4
4	129	0.46	0.77	16	empty

Interfaces

1 interface between chains.

A–E · 470 Å² buried · 5 hydrogen bonds · protein-nucleic

Compared structures

4A15 · Crystal structure of an XPD DNA complex · the same entry in another collection · chain A against A, TM-score 1.00
Q9HM14 · AlphaFold monomer V2.0 prediction for ATP-dependent DNA helicase TA0057 (Q9HM14) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9HM14
Elsewhere: RCSB PDB 4A15 · PDBe 4A15 · UniProt Q9HM14

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