GL1X · GenesisL1 explorer

MolNFT v1 · #164221 · protein

Mouse dctpase in complex with dcmpnpp

6SQZ · Dctp pyrophosphatase 1: “Mouse dctpase in complex with dcmpnpp”. X-ray diffraction, 2 ligands (0KX, MG), 2 pockets (best druggability 0.36). MolNFT v1 #164221 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
6SQZ
Type
protein
Length
224 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Dctp pyrophosphatase 1
EC
3.6.1.12
UniProt
Q9QY93
Ligands
0KX, MG
Pockets
2 · best druggability 0.36

Structure

x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADctp pyrophosphatase 1 (EC 3.6.1.12)protein11471% helix, 0% strandQ9QY93
DDctp pyrophosphatase 1 (EC 3.6.1.12)protein11071% helix, 0% strandQ9QY93

Ligands and binding sites

  • 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · 2 copies · chains A, D
  • MG · Magnesium ion · metal · 4 copies · chains A, D

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1540.360.7911empty
2630.360.7814empty

Interfaces

1 interface between chains.

  • A–D · 767 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

  • 6SQZ · Mouse dCTPase in complex with dCMPNPP · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9QY93 · AlphaFold monomer V2.0 prediction for dctp pyrophosphatase 1 (Q9QY93) · a predicted model of the same protein · chain D against A, TM-score 0.99

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