MolNFT v1 · #95462 · protein + DNA

Polymerase-DNA complex

4IR1 · DNA polymerase IV: “Polymerase-DNA complex”. X-ray diffraction, 2 ligands (1FZ, MG), 7 pockets (best druggability 0.82). MolNFT v1 #95462 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4IR1
Type: protein + DNA
Length: 751 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: 1FZ, MG
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F, A	DNA polymerase IV (EC 2.7.7.7)	protein	342	41% helix, 23% strand	Q47155
G, B	DNA (5'- D(TPCPTPAPGPGPGPTPCPCPTPAPGPGPAPCPCPC)-3')	dna	18	—	—
H	DNA (5'-D(GPGPGPTPCPCPTPAPGPGPAPCPCPC)-3')	dna	14	—	—
C	DNA (5'- D(CPTPAPGPGPGPTPCPCPTPAPGPGPAPCPCP*C)-3')	dna	17	—	—

Ligands and binding sites

1FZ · 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine · ligand · 2 copies · chains F, G, H, A, B, C
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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1004	0.82	0.83	78	1FZ, MG
2	1096	0.80	0.81	80	1FZ, MG
3	663	0.77	0.83	51	empty
4	574	0.74	0.82	50	empty
5	97	0.38	0.75	16	empty

Interfaces

9 interfaces between chains.

A–B · 1021 Å² buried · 25 hydrogen bonds · protein-nucleic
F–G · 938 Å² buried · 22 hydrogen bonds · protein-nucleic
B–C · 647 Å² buried · 65 hydrogen bonds · nucleic-nucleic
G–H · 631 Å² buried · 60 hydrogen bonds · nucleic-nucleic
F–H · 597 Å² buried · 22 hydrogen bonds · protein-nucleic

Compared structures

4IR1 · Polymerase-DNA Complex · the same entry in another collection · chain C against C, 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 4IR1 · PDBe 4IR1 · UniProt Q47155

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