SMTL ID : 5o44.1

Crystal structure of unbranched mixed tri-Ubiquitin chain containing K48 and K63 linkages.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.14 Å

Oligo State

hetero-4-4-4-mer

Ligands

18 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: R.42, Q.49, R.72 Chain B: R.42, Q.49, R.72 Ligand excluded by PLIP SO4.2: 1 residues within 4Å: Chain A: R.54 Ligand excluded by PLIP SO4.4: 8 residues within 4Å: Chain C: I.44, F.45, A.46, G.47, H.68 Chain L: F.45, S.65, T.66 Ligand excluded by PLIP SO4.5: 10 residues within 4Å: Chain B: F.45, N.60, Q.62, S.65 Chain C: R.72, R.74 Chain J: I.44, A.46, G.47, H.68 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain C: T.9, K.11, E.34 Chain G: L.73, R.74 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain D: R.42, Q.49, R.72 Chain E: R.42, Q.49, R.72 Ligand excluded by PLIP SO4.9: 1 residues within 4Å: Chain D: R.54 Ligand excluded by PLIP SO4.11: 8 residues within 4Å: Chain F: I.44, F.45, A.46, G.47, H.68 Chain I: F.45, S.65, T.66 Ligand excluded by PLIP SO4.12: 10 residues within 4Å: Chain E: F.45, N.60, Q.62, S.65 Chain F: R.72, R.74 Chain G: I.44, A.46, G.47, H.68 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain F: T.9, K.11, E.34 Chain J: L.73, R.74 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain G: R.42, Q.49, R.72, R.74 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain F: R.42, Q.49, R.72 Chain G: R.72 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain H: R.54, D.58 Ligand excluded by PLIP SO4.19: 6 residues within 4Å: Chain H: R.42, Q.49, R.72 Chain I: R.42, Q.49, R.72 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain J: R.42, Q.49, R.72, R.74 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain C: R.42, Q.49, R.72 Chain J: R.72 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain K: R.54, D.58 Ligand excluded by PLIP SO4.24: 6 residues within 4Å: Chain K: R.42, Q.49, R.72 Chain L: R.42, Q.49, R.72 Ligand excluded by PLIP

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain B: T.55, S.57, D.58 Chain C: E.24 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: S.57 Chain C: E.24, D.39, D.52 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.24, C:D.52 MG.10: 4 residues within 4Å: Chain E: T.55, S.57, D.58 Chain F: E.24 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain E: S.57 Chain F: E.24, D.39, D.52 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.24, F:D.52 MG.17: 3 residues within 4Å: Chain E: F.4 Chain G: E.64, T.66 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.64 MG.22: 3 residues within 4Å: Chain B: F.4 Chain J: E.64, T.66 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:E.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Padala, P. et al., The Crystal Structure and Conformations of an Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages. J. Mol. Biol. (2017)

Release Date

2017-11-08

Peptides

Polyubiquitin-B: ADHK
Polyubiquitin-B: BEIL
Ubiquitin: CFGJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

D
C

H
B

K
B

B
D

E
D

I
F

L
F

C
E

F
E

G
A

J
A

Polyubiquitin-B

Polyubiquitin-B

Ubiquitin

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