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SMTL ID : 2jf5.1

crystal structure of Lys63-linked di-ubiquitin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x CD: CADMIUM ION(Non-covalent)

CD.1:	2 residues within 4Å: Chain A: E.18, D.21 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.18, A:D.21
CD.3:	4 residues within 4Å: Chain B: E.18, D.21, K.29 Ligands: CL.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.21, B:D.21

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

2 residues within 4Å:

Chain A: M.1, E.16

2 PLIP interactions:

1 interactions with chain A, 1 Ligand-Water interactions

Metal complexes: A:E.16, H₂O.1

2 x CO: COBALT (II) ION(Non-covalent)

CO.4:	2 residues within 4Å: Chain B: M.1, E.16 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.16, B:E.16, H₂O.3
CO.6:	1 residues within 4Å: Chain B: E.64 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.64, H₂O.3

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

CL.5:

5 residues within 4Å:

Chain B: E.16, E.18, D.21, K.29
Ligands: CD.3

Ligand excluded by PLIP

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Komander, D. et al., Molecular Discrimination of Structurally Equivalent Lys 63-Linked and Linear Polyubiquitin Chains. Embo Rep. (2009)

Release Date

2008-02-05

Peptides

UBIQUITIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

UBIQUITIN

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