MolNFT v1 · #91388 · protein + DNA

DPO4 polymerase pre-insertion binary complex with the N- (deoxyguanosin-8-yl)-1-aminopyrene lesion

4FBU · DNA polymerase IV: “DPO4 polymerase pre-insertion binary complex with the N- (deoxyguanosin-8-yl)-1-aminopyrene lesion”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.78). MolNFT v1 #91388 on GenesisL1: 3D…

PDB: 4FBU
Type: protein + DNA
Length: 736 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase IV; DNA primer; DNA template
EC: 2.7.7.7
UniProt: Q97W02
Ligands: CA
Pockets: 9 · best druggability 0.78

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA polymerase IV (EC 2.7.7.7)	protein	341	41% helix, 23% strand	Q97W02
P, D	DNA primer	dna	13	—	—
T, C	DNA template	dna	14	—	—

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains A, P, B, D

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

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	957	0.78	0.81	59	empty
2	942	0.77	0.80	60	empty
3	471	0.76	0.84	39	empty
4	354	0.66	0.80	38	empty
5	268	0.65	0.82	30	empty

Interfaces

7 interfaces between chains.

B–C · 947 Å² buried · 19 hydrogen bonds · protein-nucleic
A–T · 917 Å² buried · 11 hydrogen bonds · protein-nucleic
A–P · 788 Å² buried · 15 hydrogen bonds · protein-nucleic
B–D · 785 Å² buried · 21 hydrogen bonds · protein-nucleic
D–C · 644 Å² buried · 58 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

4FBU · Dpo4 polymerase pre-insertion binary complex with the… · the same entry in another collection · chain C against C, 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 0.97

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 4FBU · PDBe 4FBU · UniProt Q97W02

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