5YJY	Oxidoreductase	date	Oct 11, 2017
title	Structure Of The Ndi1 Protein From Saccharomyces Cerevisiae With Ac0-12.
authors	T.Yamasita, D.K.Inaoka, T.Shiba, T.Oohashi, S.Iwata, T.Yagi, H.Kos S.Harada, K.Kita, K.Hirano
compound		source
Molecule: Rotenone-Insensitive Nadh-Ubiquinone Oxidoreducta Mitochondrial; Chain: A Fragment: Unp Residues 29-513 Synonym: Internal Nadh Dehydrogenase,Nadh:Ubiquinone Reduct Electrogenic); Ec: 1.6.5.9 Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: Atcc 204508 S288c Gene: Ndi1, Yml120c, Ym7056.06c Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Rotenone-Insensitive Nadh-Ubiquinone Oxidoreducta Mitochondrial; Chain: B Fragment: Unp Residues 28-513 Synonym: Internal Nadh Dehydrogenase,Nadh:Ubiquinone Reduct Electrogenic); Ec: 1.6.5.9 Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: Atcc 204508 S288c Gene: Ndi1, Yml120c, Ym7056.06c Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 21 21 21	R_factor 0.207 R_Free 0.299
crystal cell	length a length b length c angle alpha angle beta angle gamma 69.854 115.795 166.499 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.40 Å
ligand	8WF, FAD, MES, MG	enzyme	Oxidoreductase E.C.1.6.5.9 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Ubiquinone binding site of yeast NADH dehydrogenase revealed by structures binding novel competitive- and mixed-type inhibitors., Yamashita T, Inaoka DK, Shiba T, Oohashi T, Iwata S, Yagi T, Kosaka H, Miyoshi H, Harada S, Kita K, Hirano K, Sci Rep. 2018 Feb 5;8(1):2427. doi: 10.1038/s41598-018-20775-6. PMID:29402945

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (159 Kb) [Save to disk] Biological Unit Coordinates (5yjy.pdb1.gz) 151 Kb LPC: Ligand-Protein Contacts for 5YJY CSU: Contacts of Structural Units for 5YJY Structure Factors (525 Kb) Retrieve 5YJY in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5YJY from S2C, [Save to disk]

View 5YJY in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 5YJY

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5yjy_A] [5yjy_B] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 5YJY

Community annotation for 5YJY at PDBWiki (http://pdbwiki.org)

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---