SMTL ID : 7nbb.2 (1 other biounit)

Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with synthetic nanobody NbSL3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-1-2-1-mer

Ligands

3 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain B: I.44, H.68 Chain C: I.44, H.68 Ligands: GOL.3 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Metal complexes: C:H.68, B:H.68 MG.10: 1 residues within 4Å: Chain D: E.88 No protein-ligand interaction detected (PLIP)

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

CL.2: 3 residues within 4Å: Chain A: L.15, E.16, K.33 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain B: I.13, T.14, K.33 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain C: Q.40, L.73, R.74 Chain D: W.106 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain C: L.15, E.16, K.29 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: F.45 Chain C: F.45, S.65, T.66 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 12 residues within 4Å: Chain B: I.44, F.45, A.46, G.47, T.66, H.68 Chain C: I.44, F.45, A.46, G.47, H.68 Ligands: MG.5 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:A.46, C:G.47, B:G.47 Water bridges: C:T.66, B:A.46

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

NA.9: 4 residues within 4Å: Chain B: L.8 Chain C: Q.49 Chain D: G.101, D.102 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.49, D:D.102, D:D.102

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

2022-08-10

Peptides

Polyubiquitin-B: A
Polyubiquitin-B: BC
Synthetic nanobody NbSL3: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Polyubiquitin-B

Polyubiquitin-B

Synthetic nanobody NbSL3

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