SMTL ID : 8a67.1 (1 other biounit)

Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with matured synthetic nanobody NbSL3.3Q (3rd generation)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

hetero-1-2-1-mer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain B: I.44, F.45, A.46, G.47, H.68 Chain C: I.44, F.45, A.46, G.47, H.68 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:A.46, B:G.47, C:G.47 Water bridges: B:T.66, B:H.68, C:A.46

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.2: 2 residues within 4Å: Chain C: F.4, T.14 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain D: H.144, H.146, H.148 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.144, D:H.146, D:H.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lange, S.M. et al., VCP/p97-associated proteins are binders and debranching enzymes of K48-K63-branched ubiquitin chains. Nat.Struct.Mol.Biol. (2024)

Release Date

2023-02-15

Peptides

Polyubiquitin-B: A
Polyubiquitin-B: BC
Synthetic Nanobody NbSL3.3Q: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Polyubiquitin-B

Polyubiquitin-B

Synthetic Nanobody NbSL3.3Q

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