SMTL ID : 9ewp.1

Crystal structure of yeast E2 Ubiquitin-conjugating enzyme Ubc6 UBC domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.21 Å

Oligo State

monomer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: C.87, L.88, S.89, H.94, F.114, E.119, T.121 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.94, A:E.119, A:T.121 EDO.2: 4 residues within 4Å: Chain A: K.81, P.82, N.83, T.84 No protein-ligand interaction detected (PLIP) EDO.3: 1 residues within 4Å: Chain A: D.171 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.171, A:D.171

4 x CD: CADMIUM ION(Non-covalent)

CD.4: 3 residues within 4Å: Chain A: E.163, E.166 Ligands: CD.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.163, A:E.166 CD.5: 4 residues within 4Å: Chain A: E.163, E.166, K.167 Ligands: CD.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.163, A:E.166 CD.6: 5 residues within 4Å: Chain A: H.94, D.96, T.97 Ligands: CL.10, CL.11 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.94, A:D.96, A:D.96, H2O.3 CD.7: 1 residues within 4Å: Chain A: H.130 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.130

2 x NA: SODIUM ION(Non-functional Binders)

NA.8: 1 residues within 4Å: Chain A: D.32 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.31, A:D.32 NA.9: 1 residues within 4Å: Chain A: E.31 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.31

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 4 residues within 4Å: Chain A: H.94, D.96 Ligands: CD.6, CL.11 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: H.94, D.96, T.97 Ligands: CD.6, CL.10 Ligand excluded by PLIP CL.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Swarnkar, A. et al., Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes. Embo J. (2024)

Release Date

2024-11-20

Peptides

Ubiquitin-conjugating enzyme E2 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ubiquitin-conjugating enzyme E2 6

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