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Rat NTPDASE2 in complex with ca umppnp

Analyse Rat NTPDASE2 in complex with ca umppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4BR2
Type
protein
Length
420 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Ectonucleoside triphosphate diphosphohydrolase 2
EC
3.6.1.-, 3.6.1.5
UniProt
O35795
Ligands
UNP, CA
Pockets
4 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AEctonucleoside triphosphate diphosphohydrolase 2 (EC 3.6.1.-, 3.6.1.5)protein42041% helix, 24% strandO35795

Ligands and binding sites

  • UNP · 5'-O-[(R)-hydroxy{[(s)-hydroxy(phosphonoamino) phosphoryl]oxy}phosphoryl]uridine · ligand · chains A
  • CA · Calcium ion · metal · chains A
  • GOL · Glycerol · additive · 7 copies · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13670.670.8148UNP, CA
23290.540.7435GOL
3530.330.7714GOL
4540.290.7414empty

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

  • 4BR2 · rat NTPDase2 in complex with Ca UMPPNP · the same entry in another collection · chain A against A, TM-score 1.00
  • O35795 · AlphaFold monomer V2.0 prediction for ectonucleoside triphosphate diphosphohydrolase 2… · a predicted model of the same protein · chain A against A, TM-score 0.90

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