MolNFT v1 · #92878 · protein + DNA

DNA ligase a in complex with inhibitor

4GLX · DNA (26-mer): “DNA ligase a in complex with inhibitor”. X-ray diffraction, 3 ligands (0XS, ZN, SO4), 9 pockets (best druggability 0.82). MolNFT v1 #92878 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4GLX
Type: protein + DNA
Length: 625 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (26-mer); DNA (5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*CP*C)-3'); DNA…
EC: 6.5.1.2
UniProt: P15042
Ligands: 0XS, ZN, SO4
Pockets: 9 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	DNA (26-mer)	dna	26	—	—
C	DNA (5'-D(APCPAPAPTPTPGPCPGPAPCPCP*C)-3')	dna	13	—	—
D	DNA (5'-D(PCPAPCPTPAPTPCPGPGPAPAPTP*G)-3')	dna	13	—	—
A	DNA ligase (EC 6.5.1.2)	protein	573	40% helix, 23% strand	P15042

Ligands and binding sites

0XS · 2-amino-6-bromo-7-(trifluoromethyl)-1,8-naphthyridine-3-carboxamide · ligand · chains A
ZN · Zinc ion · metal · chains A
SO4 · Sulfate ion · ion · chains A

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	971	0.82	0.84	64	empty
2	419	0.78	0.86	45	0XS
3	642	0.75	0.82	49	empty
4	203	0.74	0.91	33	empty
5	348	0.64	0.79	30	empty

Interfaces

6 interfaces between chains.

B–A · 1574 Å² buried · 39 hydrogen bonds · protein-nucleic
C–A · 780 Å² buried · 18 hydrogen bonds · protein-nucleic
D–A · 750 Å² buried · 11 hydrogen bonds · protein-nucleic
B–D · 632 Å² buried · 51 hydrogen bonds · nucleic-nucleic
B–C · 603 Å² buried · 56 hydrogen bonds · nucleic-nucleic

Compared structures

4GLX · DNA ligase A in complex with inhibitor · the same entry in another collection · chain B against B, TM-score 1.00
P15042 · AlphaFold monomer V2.0 prediction for DNA ligase (P15042) · a predicted model of the same protein · chain A against A, TM-score 0.48

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 P15042
Elsewhere: RCSB PDB 4GLX · PDBe 4GLX · UniProt P15042

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