OCA Atlas for 1NI4

1NI4

Oxidoreductase

date

Dec 20, 2002

title

Human Pyruvate Dehydrogenase

authors

E.Ciszak, L.G.Korotchkina, P.M.Dominiak, S.Sidhu, M.S.Patel

compound

source

Molecule: Pyruvate Dehydrogenase E1 Component: Alpha Subunit;
Chain: A, C
Synonym: Pdhe1-A Type I
Ec: 1.2.4.1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dl41
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe-9

Molecule: Pyruvate Dehydrogenase E1 Component: Beta Subunit;
Chain: B, D
Synonym: Pdhe1-B
Ec: 1.2.4.1
Engineered: Yes
Mutation: Yes

symmetry

Space Group: P 21 21 21

R_factor

0.202

R_Free

0.244

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
64.337	126.889	190.638	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

1.95 Å

ligand

K, MG, MSE, TPP

enzyme

Oxidoreductase E.C.1.2.4.1 BRENDA

Gene
Ontology

Chain	Function	Process	Component
A, D, C, B	pyruvate dehydrogenase activ... pyruvate dehydrogenase (acet... oxidoreductase activity	carbohydrate metabolic proce... glucose metabolic process acetyl-CoA biosynthetic proc... pyruvate metabolic process tricarboxylic acid cycle regulation of acetyl-CoA bio... small molecule metabolic pro... oxidation-reduction process	mitochondrion mitochondrial matrix pyruvate dehydrogenase compl...

Primary reference

Structural basis for flip-flop action of thiamin pyrophosphate-dependent enzymes revealed by human pyruvate dehydrogenase., Ciszak EM, Korotchkina LG, Dominiak PM, Sidhu S, Patel MS, J Biol Chem 2003 Jun 6;278(23):21240-6. PMID:12651851

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (244 Kb) [Save to disk]

Biological Unit Coordinates (1ni4.pdb1.gz) 234 Kb

LPC: Ligand-Protein Contacts for 1NI4

CSU: Contacts of Structural Units for 1NI4

Likely Quarternary Molecular Structure file(s) for 1NI4

Structure Factors (2970 Kb)

Retrieve 1NI4 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1NI4 from S2C, [Save to disk]

Re-refined 1ni4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1NI4 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.

On AstexViewer, from MSD-EBI (viewer documentation).

On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 1NI4

Cartoon representation from PDB Cartoon

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

Crystal Contacts, from CryCo at Weizmann Institute

3D motif for 1NI4, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1ni4a_, region A [Jmol] [rasmolscript] [script source]
- Domain d1ni4b1, region B:0-191 [Jmol] [rasmolscript] [script source]
- Domain d1ni4b2, region B:192-329 [Jmol] [rasmolscript] [script source]
- Domain d1ni4c_, region C [Jmol] [rasmolscript] [script source]
- Domain d1ni4d1, region D:0-191 [Jmol] [rasmolscript] [script source]
- Domain d1ni4d2, region D:192-329 [Jmol] [rasmolscript] [script source]

Fold representative 1ni4 from FSSP and Dali (Families of Structurally Similar Proteins)

Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH

Summaries and structural analyses of PDB data files from PDBSum

Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ni4_A] [1ni4_B] [1ni4_C] [1ni4_D]

SWISS-PROT database: [P08559] [P11177]

Domain organization of [ODPA_HUMAN] [ODPB_HUMAN] by SWISSPFAM

Domain found in 1NI4: [Transket_pyr ] by SMART

Alignments of the sequence of 1NI4 with the sequences similar proteins can be viewed for 1NI4's classification [ODPA_HUMAN] [ODPB_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.

A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [ODPA_HUMAN] [ODPB_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 1NI4

Community annotation for 1NI4 at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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