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Complex of DNA polymerase IV and L-DNA duplex

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

PDB: 6L97
Type: protein + DNA
Length: 700 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.362
Source: Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)…
Molecule: DNA polymerase IV; DNA (5'-D(P*(0DG)P*(0DG)P*(0DA)P*(0DA)P*(0DT)P*(0DC)P*(0DC)P*(0DT)P*(0D…
EC: 2.7.7.7
UniProt: Q97W02
Pockets: 7 · best druggability 0.73

Structure

x-ray diffraction · resolution 2.362 · 3 distinct chains · 42% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase IV (EC 2.7.7.7)	protein	335	44% helix, 24% strand	Q97W02
B	DNA polymerase IV (EC 2.7.7.7)	protein	337	40% helix, 23% strand	Q97W02
T, P	DNA (5'-D(P(0DG)P(0DG)P(0DA)P(0DA)P(0DT)P(0DC)P(0DC)P(0DT)P(0DT)P(0DC)P(0DC)P(0DC)P(0DC)P(0DC))-3')	dna	14	—	—

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1138	0.73	0.77	57	empty
2	394	0.57	0.75	36	empty
3	89	0.38	0.76	24	empty
4	86	0.34	0.75	15	empty
5	69	0.31	0.75	19	empty

Interfaces

6 interfaces between chains.

A–B · 1232 Å² buried · 23 hydrogen bonds · protein-protein
T–P · 593 Å² buried · 57 hydrogen bonds · nucleic-nucleic
A–P · 167 Å² buried · 0 hydrogen bonds · protein-nucleic
B–P · 159 Å² buried · 3 hydrogen bonds · protein-nucleic
A–T · 84 Å² buried · 1 hydrogen bond · protein-nucleic

Modifications

Observed in the structure: 28 modified (nucleotide modification).

Compared structures

6L97 · Complex of DNA polymerase IV and L-DNA duplex · the same entry in another collection · chain A against A, 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 0.71

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 6L97 · PDBe 6L97 · UniProt Q97W02

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