MolNFT v1 · #92306 · protein + DNA

Crystal structure of DPO4 in complex with DNA duplex

4G3I: “Crystal structure of DPO4 in complex with DNA duplex”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.82). MolNFT v1 #92306 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4G3I
Type: protein + DNA
Length: 719 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA; DNA polymerase IV
EC: 2.7.7.7
UniProt: Q97W02
Ligands: CA
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 44% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, E	DNA	dna	10	—	—
D, F	DNA	dna	8	—	—
A	DNA polymerase IV (EC 2.7.7.7)	protein	342	43% helix, 25% strand	Q97W02
B	DNA polymerase IV (EC 2.7.7.7)	protein	341	45% helix, 23% strand	Q97W02

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains C, A, E, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	937	0.82	0.84	75	empty
2	943	0.78	0.80	68	empty
3	464	0.69	0.80	43	empty
4	422	0.69	0.81	42	empty
5	373	0.59	0.76	34	empty

Interfaces

7 interfaces between chains.

C–A · 762 Å² buried · 12 hydrogen bonds · protein-nucleic
D–A · 750 Å² buried · 18 hydrogen bonds · protein-nucleic
E–B · 740 Å² buried · 13 hydrogen bonds · protein-nucleic
A–B · 687 Å² buried · 5 hydrogen bonds · protein-protein
F–B · 659 Å² buried · 12 hydrogen bonds · protein-nucleic

Compared structures

4G3I · Crystal structure of Dpo4 in complex with DNA duplex · 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 A against A, TM-score 0.96

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 4G3I · PDBe 4G3I · UniProt Q97W02

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