Research workbench

XPD_APO

Analyse XPD_APO in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CRW
Type: protein
Length: 485 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: XPD/RAD3 related DNA helicase
EC: 3.-.-.-
UniProt: Q4JC68
Ligands: FC6
Pockets: 6 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	XPD/RAD3 related DNA helicase (EC 3.-.-.-)	protein	485	36% helix, 18% strand	Q4JC68

Ligands and binding sites

FC6 · Hexacyanoferrate(3-) · ligand · chains 1

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1050	0.85	0.86	120	FC6
2	317	0.67	0.82	31	empty
3	89	0.43	0.78	14	empty
4	65	0.36	0.78	11	empty
5	96	0.32	0.73	21	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

3CRW · XPD_APO · the same entry in another collection · chain 1 against 1, TM-score 1.00
Q4JC68 · AlphaFold monomer V2.0 prediction for ATP-dependent DNA helicase SACI_0192 (Q4JC68) · a predicted model of the same protein · chain 1 against A, TM-score 0.99

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 Q4JC68
Elsewhere: RCSB PDB 3CRW · PDBe 3CRW · UniProt Q4JC68

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