SMTL ID : 8kev.1

Cryo-EM structure of HRD1-SEL1L-XTP3B (state D1) complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.50 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x ALA- ASN- ALA: Ala-Asn-Ala(Non-functional Binders)

ALA-ASN-ALA.1: 1 residues within 4Å: Ligands: NAG-NAG-MAN-MAN-MAN-MAN-MAN.3 No protein-ligand interaction detected (PLIP) ALA-ASN-ALA.2: 1 residues within 4Å: Ligands: NAG-NAG-MAN-MAN-MAN-MAN-MAN.4 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-4)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN-MAN-MAN-MAN.3: 11 residues within 4Å: Chain A: K.688, D.692, E.696 Chain B: S.119, Y.120, W.121, Q.133, L.201, R.207, Y.234 Ligands: ALA-ASN-ALA.1 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN-MAN-MAN-MAN.4: 10 residues within 4Å: Chain C: K.688, R.689, D.692 Chain D: S.119, Y.120, W.121, Y.123, R.207, C.232 Ligands: ALA-ASN-ALA.2 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:S.119

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.5: 2 residues within 4Å: Chain A: N.217, K.248 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.248 NAG.6: 1 residues within 4Å: Chain A: N.272 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.272 NAG.7: 2 residues within 4Å: Chain A: E.607, N.608 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.607 NAG.8: 2 residues within 4Å: Chain C: N.217, K.248 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain C: N.272 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.272 NAG.10: 1 residues within 4Å: Chain C: N.608 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, L. et al., Structural insights into the human HRD1 ubiquitin ligase complex. Nat Commun (2025)

Release Date

2025-02-19

Peptides

Protein sel-1 homolog 1: AC
Endoplasmic reticulum lectin 1: BD
E3 ubiquitin-protein ligase synoviolin: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

C
C

B
E

D
F

E
A

F
B

Protein sel-1 homolog 1

Endoplasmic reticulum lectin 1

E3 ubiquitin-protein ligase synoviolin

Related Entries With Identical Sequence