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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-1-2-1-mer

Ligands

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

MG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.2: 1 residues within 4Å: Chain A: D.32 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.32, H2O.1, H2O.1, H2O.2, H2O.3 MG.6: 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.8: 1 residues within 4Å: Chain D: E.88 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 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 Ligands: MG.6 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:A.46, C:G.47, C:H.68, B:G.47 Water bridges: B:A.46

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

CL.4: 4 residues within 4Å: Chain C: Q.40, L.73, R.74 Chain D: W.106 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain D: L.20, R.21 Ligand excluded by PLIP

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

NA.5: 3 residues within 4Å: Chain C: A.28, Q.31, D.32 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lange, S.M. et al., Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with synthetic nanobody NbSL3. To Be Published

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
A

B
B

C
C

D
D

Polyubiquitin-B

Polyubiquitin-B

Synthetic nanobody NbSL3

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