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Efficient and high fidelity incorporation of dctp opposite 7,8-dihydro-8-oxodeoxyguanosine by sulfolobus solfataricus DNA polymerase DPO4

Analyse Efficient and high fidelity incorporation of dctp opposite… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2C2R
Type: protein + DNA
Length: 371 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase IV; 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*C)-3'; 5'-D(*TP*CP*AP*C…
EC: 2.7.7.7
UniProt: Q97W02
Ligands: DCT, CA
Pockets: 3 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase IV (EC 2.7.7.7)	protein	341	41% helix, 25% strand	Q97W02
P	5'-D(GPGPGPGPGPAPAPGPGPAP TPTP*C)-3'	dna	14	—	—
T	5'-D(TPCPAPC 8OGPGPAPAPTPCPCP TPTPCPCPCPCP*C)-3'	dna	16	—	—

Ligands and binding sites

DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · chains A, P, T
CA · Calcium ion · metal · 4 copies · chains A, P

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1107	0.82	0.83	88	DCT, CA
2	73	0.42	0.81	17	empty
3	116	0.42	0.77	18	empty

Interfaces

3 interfaces between chains.

A–T · 1053 Å² buried · 22 hydrogen bonds · protein-nucleic
A–P · 714 Å² buried · 19 hydrogen bonds · protein-nucleic
P–T · 640 Å² buried · 55 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

2C2R · Efficient and High Fidelity Incorporation of dCTP Opposite 7,8… · the same entry in another collection · chain A against A, 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 0.97

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 Q97W02
Elsewhere: RCSB PDB 2C2R · PDBe 2C2R · UniProt Q97W02

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