MolNFT v1 · #71514 · protein + DNA

Ternary complex of a DNA polymerase lambda loop mutant

3MGI: “Ternary complex of a DNA polymerase lambda loop mutant”. X-ray diffraction, 3 ligands (D3T, MG, NA), 3 pockets (best druggability 0.68). MolNFT v1 #71514 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3MGI
Type: protein + DNA
Length: 340 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase lambda; DNA; DNA (5'-D(*CP*AP*GP*TP*AP*T)-3'); DNA (5'-D(P*GP*CP*CP*G)-3')
EC: 2.7.7.7, 4.2.99.-
UniProt: Q9UGP5
Ligands: D3T, MG, NA
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-)	protein	319	48% helix, 15% strand	Q9UGP5
T	DNA	dna	11	—	—
P	DNA (5'-D(CPAPGPTPAPT)-3')	dna	6	—	—
D	DNA (5'-D(PGPCPCPG)-3')	dna	4	—	—

Ligands and binding sites

D3T · 2',3'-dideoxy-thymidine-5'-triphosphate · ligand · chains A, T, P
MG · Magnesium ion · metal · chains A
NA · Sodium ion · metal · chains A, P

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

Pockets

3 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	571	0.68	0.78	48	D3T, MG, NA
2	146	0.52	0.80	23	empty
3	176	0.48	0.77	22	empty

Interfaces

5 interfaces between chains.

A–T · 861 Å² buried · 18 hydrogen bonds · protein-nucleic
A–P · 381 Å² buried · 11 hydrogen bonds · protein-nucleic
A–D · 377 Å² buried · 14 hydrogen bonds · protein-nucleic
T–P · 285 Å² buried · 21 hydrogen bonds · nucleic-nucleic
T–D · 190 Å² buried · 17 hydrogen bonds · nucleic-nucleic

Compared structures

3MGI · Ternary complex of a DNA polymerase lambda loop mutant · the same entry in another collection · chain A against A, TM-score 1.00
Q9UGP5 · AlphaFold monomer V2.0 prediction for DNA polymerase lambda (Q9UGP5) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9UGP5
Elsewhere: RCSB PDB 3MGI · PDBe 3MGI · UniProt Q9UGP5

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