MolNFT v1 · #32841 · protein + DNA

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

2C2D · DNA polymerase IV: “Efficient and high fidelity incorporation of dctp opposite 7,8-dihydro-8-oxodeoxyguanosine by sulfolobus…”. X-ray diffraction, 2 ligands (DTP, CA), 2 pockets (best druggability 0.77). MolNFT v1 #32841 on…

PDB: 2C2D
Type: protein + DNA
Length: 369 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: DTP, CA
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase IV (EC 2.7.7.7)	protein	341	43% helix, 24% strand	Q97W02
P	5'-D(GPGPGPGPGPAPAPGPGPAP TPTP*C)-3'	dna	13	—	—
T	5'-D(TPCPAPC 8OGPGPAPAPTPCPCP TPTPCPCPCPCP*C)-3'	dna	15	—	—

Ligands and binding sites

DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains A, P, T
CA · Calcium ion · metal · 5 copies · chains A

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

Pockets

2 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	1174	0.77	0.79	77	DTP, CA
2	379	0.71	0.83	34	empty

Interfaces

3 interfaces between chains.

A–T · 887 Å² buried · 13 hydrogen bonds · protein-nucleic
P–T · 556 Å² buried · 41 hydrogen bonds · nucleic-nucleic
A–P · 545 Å² buried · 14 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

2C2D · 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 0.98

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 2C2D · PDBe 2C2D · UniProt Q97W02

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