3EXG	Oxidoreductase	date	Oct 16, 2008
title	Crystal Structure Of The Pyruvate Dehydrogenase (E1p) Compon Human Pyruvate Dehydrogenase Complex
authors	M.Kato, R.M.Wynn, J.L.Chuang, S.C.Tso, M.Machius, J.Li, D.T.Chuan
compound		source
Molecule: Pyruvate Dehydrogenase E1 Component Subunit Alpha Form, Mitochondrial; Chain: A, C, E, G, I, K, M, O, Q, S, U, W, Y, 1, 3, 5 Fragment: E1p-Alpha Synonym: Pyruvate Dehydrogenase (E1p) Alpha Subunit; Pdhe1- Ec: 1.2.4.1 Engineered: Yes Mutation: Yes Other_details: Phosphorylation Site 1 (S264) Only Mutant (S203as271a) With The Site 1 Being Phosphorylated. Apo For		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Pdha1, Phe1a Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid
Molecule: Pyruvate Dehydrogenase E1 Component Subunit Beta, Mitochondrial; Chain: B, D, F, H, J, L, N, P, R, T, V, X, Z, 2, 4, 6 Fragment: E1p-Beta Synonym: Pyruvate Dehydrogenase (E1p) Beta Subunit; Pdhe1-B Ec: 1.2.4.1 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Pdhb, Phe1b Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid
symmetry	Space Group: P 1	R_factor 0.189 R_Free 0.253
crystal cell	length a length b length c angle alpha angle beta angle gamma 119.278 128.290 228.410 90.14 90.05 90.02
method	X-Ray Diffraction	resolution	3.01 Å
ligand	K	enzyme	Oxidoreductase E.C.1.2.4.1 BRENDA
Gene Ontology	Chain Function Process Component S, F, T, N, K, Y, E, 2, V, Z, Q, 1, M, C, L, 6, A, O, J, W, X, 3, P, B, H, 4, D, R, I, G, U, 5 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 inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops., Kato M, Wynn RM, Chuang JL, Tso SC, Machius M, Li J, Chuang DT, Structure. 2008 Dec 12;16(12):1849-59. PMID:19081061

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1664 Kb) [Save to disk] Biological Unit Coordinates (3exg.pdb1.gz) 223 Kb Biological Unit Coordinates (3exg.pdb2.gz) 223 Kb Biological Unit Coordinates (3exg.pdb3.gz) 224 Kb Biological Unit Coordinates (3exg.pdb4.gz) 221 Kb Biological Unit Coordinates (3exg.pdb5.gz) 223 Kb Biological Unit Coordinates (3exg.pdb6.gz) 225 Kb Biological Unit Coordinates (3exg.pdb7.gz) 223 Kb Biological Unit Coordinates (3exg.pdb8.gz) 223 Kb LPC: Ligand-Protein Contacts for 3EXG CSU: Contacts of Structural Units for 3EXG Likely Quarternary Molecular Structure file(s) for 3EXG Structure Factors (4218 Kb) Retrieve 3EXG in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3EXG from S2C, [Save to disk] Re-refined 3exg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3EXG 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 3EXG

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 3EXG, from MSDmotif at EBI Fold representative 3exg from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3exg_1] [3exg_2] [3exg_3] [3exg_4] [3exg_5] [3exg_6] [3exg_A] [3exg_B] [3exg_C] [3exg_D] [3exg_E] [3exg_F] [3exg_G] [3exg_H] [3exg_I] [3exg_J] [3exg_K] [3exg_L] [3exg_M] [3exg_N] [3exg_O] [3exg_P] [3exg_Q] [3exg_R] [3exg_S] [3exg_T] [3exg_U] [3exg_V] [3exg_W] [3exg_X] [3exg_Y] [3exg_Z] SWISS-PROT database: [P08559] [P11177] Domain organization of [ODPA_HUMAN] [ODPB_HUMAN] by SWISSPFAM Domain found in 3EXG: [Transket_pyr ] by SMART Alignments of the sequence of 3EXG with the sequences similar proteins can be viewed for 3EXG'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 3EXG

Community annotation for 3EXG at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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