MolNFT v1 · #75466 · protein + DNA

DPO4 Y12A mutant incorporating ADP opposite template dt

3PR5 · DNA polymerase IV: “DPO4 Y12A mutant incorporating ADP opposite template dt”. X-ray diffraction, 2 ligands (ATP, CA), 2 pockets (best druggability 0.81). MolNFT v1 #75466 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3PR5
Type: protein + DNA
Length: 369 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase IV; DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*C)-3'); DNA (5'…
EC: 2.7.7.7
UniProt: Q97W02
Ligands: ATP, CA
Pockets: 2 · best druggability 0.81

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	DNA polymerase IV (EC 2.7.7.7)	protein	341	43% helix, 24% strand	Q97W02
P	DNA (5'-D(GPGPGPGPGPAPAPGPGPAPCPTP*C)-3')	dna	13	—	—
T	DNA (5'- D(TPTPCPAPTPGPAPGPTPCPCPTPTPCPCPCPCPC)-3')	dna	15	—	—

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains B, P, T
CA · Calcium ion · metal · 2 copies · chains B

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	1193	0.81	0.83	80	CA, ATP
2	679	0.74	0.80	39	empty

Interfaces

3 interfaces between chains.

B–T · 948 Å² buried · 21 hydrogen bonds · protein-nucleic
P–T · 574 Å² buried · 55 hydrogen bonds · nucleic-nucleic
B–P · 556 Å² buried · 17 hydrogen bonds · protein-nucleic

Compared structures

3PR5 · Dpo4 Y12A mutant incorporating ADP opposite template dT · 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 B 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 3PR5 · PDBe 3PR5 · UniProt Q97W02

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