SMTL ID : 8a67.2 (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 CL: CHLORIDE ION(Non-functional Binders)

CL.1: 5 residues within 4Å: Chain A: K.27, P.38, D.39, D.52, R.72 Ligand excluded by PLIP

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

NA.2: 2 residues within 4Å: Chain A: E.16, E.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.16, A:E.18 NA.4: 3 residues within 4Å: Chain B: I.13, K.33, E.34 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.34, B:E.34

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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 C, 2 interactions with chain B Hydrogen bonds: C:A.46, C:G.47, C:H.68, B:A.46, B:G.47 Water bridges: C:T.66

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

IPA.5: 4 residues within 4Å: Chain D: H.144, H.146, H.148 Ligands: ZN.6 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain D: H.144, H.146, H.148 Ligands: IPA.5 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
E

B
F

C
G

D
H

Polyubiquitin-B

Polyubiquitin-B

Synthetic Nanobody NbSL3.3Q

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