MolNFT v1 · #95473 · protein + DNA

Structure of polymerase-DNA complex

4IRD · DNA (5'- D(*TP*CP*TP*TP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*…: “Structure of polymerase-DNA complex”. X-ray diffraction, 2 ligands (DZ4, MG), 7 pockets (best druggability 0.80). MolNFT v1 #95473 on GenesisL1: 3D structure, binding…

PDB: 4IRD
Type: protein + DNA
Length: 751 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*TP*CP*TP*TP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3'); DNA…
EC: 2.7.7.7
UniProt: Q47155
Ligands: DZ4, MG
Pockets: 7 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G, B	DNA (5'- D(TPCPTPTPGPGPGPTPCPCPTPAPGPGPAPCPCPC)-3')	dna	18	—	—
H	DNA (5'-D(GPGPGPTPCPCPTPAPGPGPAPCPCPC)-3')	dna	14	—	—
C	DNA (5'- D(CPTPAPGPGPGPTPCPCPTPAPGPGPAPCPCP*C)-3')	dna	17	—	—
F, A	DNA polymerase IV (EC 2.7.7.7)	protein	342	41% helix, 24% strand	Q47155

Ligands and binding sites

DZ4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · 2 copies · chains G, H, F, B, C, A
MG · Magnesium ion · metal · 4 copies · chains F, H, A, C

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

Pockets

7 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	1062	0.80	0.81	75	DZ4, MG
2	652	0.77	0.83	50	empty
3	899	0.76	0.80	56	empty
4	732	0.74	0.80	49	empty
5	217	0.63	0.83	35	DZ4, MG

Interfaces

9 interfaces between chains.

B–A · 964 Å² buried · 21 hydrogen bonds · protein-nucleic
G–F · 951 Å² buried · 16 hydrogen bonds · protein-nucleic
B–C · 640 Å² buried · 67 hydrogen bonds · nucleic-nucleic
G–H · 628 Å² buried · 60 hydrogen bonds · nucleic-nucleic
C–A · 595 Å² buried · 23 hydrogen bonds · protein-nucleic

Compared structures

4IRD · Structure of Polymerase-DNA complex · the same entry in another collection · chain A against A, TM-score 1.00
Q47155 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q47155) · a predicted model of the same protein · chain F 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 4IRD · PDBe 4IRD · UniProt Q47155

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