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MolNFT v1 · #171460 · protein

SARS-cov-2 macrodomain in complex with ADP-ribose

6Z5T · Replicase polyprotein 1AB: “SARS-cov-2 macrodomain in complex with ADP-ribose”. X-ray diffraction, 2 ligands (APR, NA), 3 pockets (best druggability 0.69). MolNFT v1 #171460 on GenesisL1: 3D structure, binding sites and pockets in…

PDB
6Z5T
Type
protein
Length
348 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Replicase polyprotein 1AB
EC
3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-
UniProt
P0DTD1
Ligands
APR, NA
Pockets
3 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BReplicase polyprotein 1AB (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-)protein17440% helix, 18% strandP0DTD1

Ligands and binding sites

  • APR · Adenosine-5-diphosphoribose · ligand · 2 copies · chains A, B
  • NA · Sodium ion · metal · 2 copies · chains A, B

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
14940.690.7951APR
22190.610.8132APR
3520.270.7413empty

Interfaces

1 interface between chains.

  • A–B · 356 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

  • 6Z5T · SARS-CoV-2 Macrodomain in complex with ADP-ribose · the same entry in another collection · chain A against A, TM-score 1.00

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