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SMTL ID : 4k7u.2 (2 other biounits)

Crystal structure of Zn2.3-hUb (human ubiquitin) adduct from a solution 70 mM zinc acetate/1.3 mM hUb

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.1:	3 residues within 4Å: Chain A: K.6, H.68 Ligands: ACT.4 3 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.68, H₂O.3, ACT.4
ZN.2:	4 residues within 4Å: Chain A: M.1, E.16, V.17 Ligands: ZN.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.16, A:E.16
ZN.3:	1 residues within 4Å: Ligands: ZN.2 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.4:

3 residues within 4Å:

Chain A: K.6, H.68
Ligands: ZN.1

2 PLIP interactions:

2 interactions with chain A

Salt bridges: A:K.6, A:H.68

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5:

3 residues within 4Å:

Chain A: K.48, Q.49, Y.59

2 PLIP interactions:

2 interactions with chain A

Hydrogen bonds: A:Q.49, A:Q.49

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Fermani, S. et al., Conformational selection of ubiquitin quaternary structures driven by zinc ions. Chemistry (2013)

Release Date

2013-05-08

Peptides

ubiquitin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
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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