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Structure of polymerase-DNA complex, DNA

Analyse Structure of polymerase-DNA complex, DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4IRK
Type: protein + DNA
Length: 748 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase IV; DNA (5'- D(*TP*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')…
EC: 2.7.7.7
UniProt: Q47155
Ligands: DCP, MG
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	DNA polymerase IV (EC 2.7.7.7)	protein	342	41% helix, 23% strand	Q47155
C, F	DNA (5'- D(TPCPTPAPGPGPGPTPCPCPTPAPGPGPAPCPCPC)-3')	dna	18	—	—
G, H	DNA (5'- D(CPTPAGPGPGPTPCPCPTPAPGPGPAPCPCP*(DOC))-3')	dna	14	—	—

Ligands and binding sites

DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 2 copies · chains B, C, G, A, F, H
MG · Magnesium ion · metal · 2 copies · chains B, A

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	996	0.82	0.83	92	DCP
2	1032	0.80	0.82	77	DCP, MG
3	825	0.77	0.81	59	empty
4	767	0.72	0.78	55	empty
5	65	0.36	0.77	14	empty

Interfaces

9 interfaces between chains.

B–C · 1011 Å² buried · 18 hydrogen bonds · protein-nucleic
A–F · 976 Å² buried · 19 hydrogen bonds · protein-nucleic
F–H · 637 Å² buried · 60 hydrogen bonds · nucleic-nucleic
C–G · 628 Å² buried · 65 hydrogen bonds · nucleic-nucleic
A–H · 594 Å² buried · 20 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

4IRK · structure of Polymerase-DNA complex, dna · the same entry in another collection · chain H against H, TM-score 1.00
Q47155 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q47155) · a predicted model of the same protein · chain A 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 Q47155
Elsewhere: RCSB PDB 4IRK · PDBe 4IRK · UniProt Q47155

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