SMTL ID : 7kag.1

Crystal structure of the ubiquitin-like domain 1 (Ubl1) of Nsp3 from SARS-CoV-2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.21 Å

Oligo State

homo-dimer

Ligands

13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: E.14, Q.16 Chain B: P.2, E.14, Q.16 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.18, B:E.14 EDO.2: 3 residues within 4Å: Chain A: E.26, F.90, Y.103 No protein-ligand interaction detected (PLIP) EDO.3: 2 residues within 4Å: Chain A: W.82, A.85 No protein-ligand interaction detected (PLIP) EDO.5: 2 residues within 4Å: Chain A: K.38, V.68 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: D.28, E.29, R.30 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: A.54, A.85, Y.87 No protein-ligand interaction detected (PLIP) EDO.8: 2 residues within 4Å: Chain A: Y.42, A.60 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain A: D.10 Chain B: K.19, L.98, A.99 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.19, A:D.10 EDO.10: 3 residues within 4Å: Chain B: E.81, W.82, A.85 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.81 EDO.11: 3 residues within 4Å: Chain B: F.90, E.92, D.110 No protein-ligand interaction detected (PLIP) EDO.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain B: P.67, V.68, S.69, E.70 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.69, B:E.70 EDO.14: 2 residues within 4Å: Chain B: D.28, R.30 No protein-ligand interaction detected (PLIP)

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: K.19, A.99, S.100 Chain B: D.9, D.10 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.10, B:D.10, A:S.100 Salt bridges: A:K.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stogios, P.J., Crystal structure of the ubiquitin-like domain 1 (Ubl1) of Nsp3 from SARS-CoV-2. To Be Published

Release Date

2020-10-14

Peptides

Non-structural protein 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Non-structural protein 3