SMTL ID : 2is9.2 (1 other biounit)

Structure of yeast DCN-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

2 x PT: PLATINUM (II) ION(Non-covalent)

PT.1: 3 residues within 4Å: Chain A: M.165 Ligands: CL.2, CL.5 No protein-ligand interaction detected (PLIP) PT.7: 3 residues within 4Å: Chain B: M.165 Ligands: CL.8, CL.11 No protein-ligand interaction detected (PLIP)

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

CL.2: 4 residues within 4Å: Chain B: E.63, D.64, S.67 Ligands: PT.1 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: L.168 Chain B: S.67, M.71 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: D.161 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: M.165 Chain B: E.63 Ligands: PT.1, MES.12 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: E.63, D.64, S.67 Ligands: PT.7 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: S.67, M.71 Chain B: L.168 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: D.161 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: E.63 Chain B: M.165 Ligands: MES.6, PT.7 Ligand excluded by PLIP

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.6: 9 residues within 4Å: Chain A: Y.6, R.62, E.63 Chain B: M.165, L.168, A.187, A.188, W.189 Ligands: CL.11 5 PLIP interactions: 5 interactions with chain A Water bridges: A:V.5, A:V.5, A:V.5 Salt bridges: A:R.62, A:E.63 MES.12: 9 residues within 4Å: Chain A: M.165, L.168, A.187, A.188, W.189 Chain B: Y.6, R.62, E.63 Ligands: CL.5 5 PLIP interactions: 5 interactions with chain B Water bridges: B:V.5, B:V.5, B:V.5 Salt bridges: B:R.62, B:E.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, X. et al., Structural basis for the function of DCN-1 in protein Neddylation. J.Biol.Chem. (2007)

Release Date

2007-06-26

Peptides

Defective in cullin neddylation protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Defective in cullin neddylation protein 1

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