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Oxog-modified preinsertion binary complex

Analyse Oxog-modified preinsertion binary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ASJ
Type: protein + DNA
Length: 734 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*(DDG))-3'; 5'-D(*CP*TP*AP*AP*CP*(8OG)…
EC: 2.7.7.7
UniProt: Q97W02
Ligands: CA
Pockets: 5 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, H	5'-D(GPGPTPTPGPGPAPTPGPGPTPAP*(DDG))-3'	dna	13	—	—
E, J	5'-D(CPTPAPAPCP(8OG) CPTPAPCPCPAPTPCPCPAPAPCP*C)-3'	dna	13	—	—
A, B	DNA polymerase IV (EC 2.7.7.7)	protein	341	44% helix, 23% strand	Q97W02

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains E, D, A, H, B

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

Pockets

5 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	1023	0.78	0.80	68	empty
2	1142	0.76	0.78	73	empty
3	1143	0.76	0.78	75	empty
4	599	0.74	0.81	39	empty
5	369	0.62	0.78	33	empty

Interfaces

6 interfaces between chains.

D–A · 821 Å² buried · 16 hydrogen bonds · protein-nucleic
H–B · 785 Å² buried · 15 hydrogen bonds · protein-nucleic
J–B · 675 Å² buried · 13 hydrogen bonds · protein-nucleic
E–A · 661 Å² buried · 17 hydrogen bonds · protein-nucleic
H–J · 605 Å² buried · 60 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

2ASJ · oxoG-modified Preinsertion Binary Complex · the same entry in another collection · chain B against B, TM-score 1.00
Q97W02 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q97W02) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q97W02
Elsewhere: RCSB PDB 2ASJ · PDBe 2ASJ · UniProt Q97W02

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