MolNFT v1 · #31393 · protein + DNA

Unmodified insertion ternary complex

2ATL · 5'-D(*GP*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*(DDG))-3': “Unmodified insertion ternary complex”. X-ray diffraction, 2 ligands (DCP, CA), 6 pockets (best druggability 0.80). MolNFT v1 #31393 on GenesisL1: 3D structure, binding sites and…

PDB: 2ATL
Type: protein + DNA
Length: 744 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*(DDG))-3'…
EC: 2.7.7.7
UniProt: Q97W02
Ligands: DCP, CA
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, H	5'-D(GPGPTPTPGPGPAPTPGPGPTPAP*(DDG))-3'	dna	13	—	—
E	5'-D(CPTAPAPCPGPCPTPAPCPCPAPTPCPCPAPAPCP* C)-3'	dna	17	—	—
J	5'-D(CPTAPAPCPGPCPTPAPCPCPAPTPCPCPAPAPCP* C)-3'	dna	19	—	—
A, B	DPO4 polymerase IV (EC 2.7.7.7)	protein	341	43% helix, 25% strand	Q97W02

Ligands and binding sites

DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 2 copies · chains D, E, A, H, J, B
CA · Calcium ion · metal · 8 copies · chains D, E, H, A, 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1156	0.80	0.82	76	CA, DCP
2	1119	0.80	0.81	83	CA, DCP
3	686	0.73	0.79	42	empty
4	595	0.72	0.80	40	empty
5	107	0.41	0.77	15	empty

Interfaces

6 interfaces between chains.

J–B · 1258 Å² buried · 25 hydrogen bonds · protein-nucleic
E–A · 1020 Å² buried · 21 hydrogen bonds · protein-nucleic
H–B · 598 Å² buried · 13 hydrogen bonds · protein-nucleic
D–E · 597 Å² buried · 59 hydrogen bonds · nucleic-nucleic
H–J · 573 Å² buried · 48 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

2ATL · Unmodified Insertion Ternary Complex · 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 B against A, TM-score 0.98

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 2ATL · PDBe 2ATL · UniProt Q97W02

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