MolNFT v1 · #180166 · protein + DNA

Human DNA ligase 1(E346A/E592A) bound to a bulged DNA substrate

7KR3: “Human DNA ligase 1(E346A/E592A) bound to a bulged DNA substrate”. X-ray diffraction, 1 ligand (AMP), 7 pockets (best druggability 0.84). MolNFT v1 #180166 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7KR3
Type: protein + DNA
Length: 669 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA ligase 1; DNA (5'-D(*AP*AP*TP*GP*TP*CP*TP*GP*CP*CP*CP*C)-3'); DNA…
EC: 6.5.1.1
UniProt: P18858
Ligands: AMP
Pockets: 7 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA ligase 1 (EC 6.5.1.1)	protein	632	38% helix, 21% strand	P18858
B	DNA (5'-D(APAPTPGPTPCPTPGPCPCPCPC)-3')	dna	12	—	—
C	DNA (5'-D(PAPTPTPCPTPGP*C)-3')	dna	7	—	—
D	DNA (5'- D(GPCPAPGPAPAPTPGPGPGPCPAPGPAPCPAPTPT)-3')	dna	18	—	—

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · chains A, B, C
ACT · Acetate ion · additive · chains B, D

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

Pockets

7 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	690	0.84	0.88	68	AMP
2	656	0.72	0.79	48	empty
3	390	0.68	0.81	39	empty
4	119	0.57	0.85	20	ACT
5	236	0.57	0.79	22	empty

Interfaces

6 interfaces between chains.

A–D · 1521 Å² buried · 34 hydrogen bonds · protein-nucleic
A–B · 713 Å² buried · 12 hydrogen bonds · protein-nucleic
A–C · 609 Å² buried · 15 hydrogen bonds · protein-nucleic
B–D · 497 Å² buried · 51 hydrogen bonds · nucleic-nucleic
C–D · 357 Å² buried · 31 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

7KR3 · Human DNA Ligase 1(E346A/E592A) Bound to a bulged DNA substrate · the same entry in another collection · chain A against A, TM-score 1.00
P18858 · AlphaFold monomer V2.0 prediction for DNA ligase 1 (P18858) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P18858
Elsewhere: RCSB PDB 7KR3 · PDBe 7KR3 · UniProt P18858

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