GL1X · GenesisL1 explorer

Research workbench

DNA polymerase lambda, TTPAS:AT CA2+ ground state ternary complex

Analyse DNA polymerase lambda, TTPAS:AT CA2+ ground state ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
7M4K
Type
protein + DNA
Length
331 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA polymerase lambda; DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3'); DNA…
EC
2.7.7.7, 4.2.99.-
UniProt
Q9UGP5
Ligands
YQS, NA, CA
Pockets
3 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA polymerase lambda (EC 2.7.7.7, 4.2.99.-)protein31052% helix, 14% strandQ9UGP5
TDNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')dna11——
PDNA (5'-D(*CP*AP*GP*TP*AP*C)-3')dna6——
DDNA (5'-D(P*GP*CP*CP*G)-3')dna4——

Ligands and binding sites

  • YQS · [[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate · ligand · chains A, T, P
  • NA · Sodium ion · metal · 4 copies · chains A, P, D
  • CA · Calcium ion · metal · chains A
  • EDO · 1,2-ethanediol · additive · 6 copies · 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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
17280.660.7546CA, EDO, YQS
21590.540.8123EDO
32410.480.7422empty

Interfaces

5 interfaces between chains.

  • A–T · 768 Ų buried · 14 hydrogen bonds · protein-nucleic
  • A–D · 380 Ų buried · 12 hydrogen bonds · protein-nucleic
  • A–P · 370 Ų buried · 15 hydrogen bonds · protein-nucleic
  • T–P · 285 Ų buried · 21 hydrogen bonds · nucleic-nucleic
  • T–D · 192 Ų buried · 18 hydrogen bonds · nucleic-nucleic

Compared structures

  • 7M4K · DNA Polymerase Lambda, TTPaS:At Ca2+ Ground State Ternary Complex · 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

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.