2NYL Hydrolase Hydrolase Inhibitor date Nov 20, 2006
title Crystal Structure Of Protein Phosphatase 2a (Pp2a) Holoenzym Catalytic Subunit Carboxyl Terminus Truncated
authors Y.Xing, Y.Xu, Y.Chen, Y.Chao, Z.Lin, Y.Shi
compound source
Molecule: Protein Phosphatase 2, Regulatory Subunit A (Pr 6 Isoform;
Chain: A, D
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ppp2r1a
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-2t

Molecule: Serinethreonine-Protein Phosphatase 2a 56 Kda Re Subunit Gamma Isoform;
Chain: B, E
Synonym: Pp2a, B Subunit, B' Gamma Isoform, Pp2a, B Subunit Gamma Isoform, Pp2a, B Subunit, Pr61 Gamma Isoform, Pp2a, B R5 Gamma Isoform, Ny-Ren-29 Antigen;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ppp2r5c, Kiaa0044
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-2t

Molecule: Serinethreonine-Protein Phosphatase 2a Catalytic Alpha Isoform;
Chain: C, F
Synonym: Pp2a-Alpha, Replication Protein C, Rp-C
Ec: 3.1.3.16
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ppp2ca
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_strain: Hi-5
Expression_system_vector_type: Virus

Molecule: Microcystin Lr
Chain: G, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Cyanobacteria
Organism_taxid: 1117
symmetry Space Group: P 21 21 21
R_factor 0.282 R_Free 0.335
crystal
cell
length a length b length c angle alpha angle beta angle gamma
108.480 159.850 270.370 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.80 Å
ligand 1ZN, ACB, ADD, DAL, DAM, DGL, FGA, MAA, MN, MSE enzyme Hydrolase E.C.3.1.3.16 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D


F, C


Primary referenceStructure of the protein phosphatase 2A holoenzyme., Xu Y, Xing Y, Chen Y, Chao Y, Lin Z, Fan E, Yu JW, Strack S, Jeffrey PD, Shi Y, Cell. 2006 Dec 15;127(6):1239-51. PMID:17174897
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (422 Kb) [Save to disk]
  • Biological Unit Coordinates (2nyl.pdb1.gz) 209 Kb
  • Biological Unit Coordinates (2nyl.pdb2.gz) 210 Kb
  • LPC: Ligand-Protein Contacts for 2NYL
  • CSU: Contacts of Structural Units for 2NYL
  • Likely Quarternary Molecular Structure file(s) for 2NYL
  • Retrieve 2NYL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2NYL from S2C, [Save to disk]
  • View 2NYL 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 2NYL
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2NYL, from MSDmotif at EBI
  • Fold representative 2nyl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2nyl_H] [2nyl_A] [2nyl_E] [2nyl_F] [2nyl_D] [2nyl_G] [2nyl] [2nyl_C] [2nyl_B]
  • SWISS-PROT database: [Q13362] [P30153] [P67775]
  • Domain organization of [2A5G_HUMAN] [2AAA_HUMAN] [PP2AA_HUMAN] by SWISSPFAM
  • Domain found in 2NYL: [PP2Ac ] by SMART
  • Alignments of the sequence of 2NYL with the sequences similar proteins can be viewed for 2NYL's classification [2A5G_HUMAN] [2AAA_HUMAN] [PP2AA_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 [2A5G_HUMAN] [2AAA_HUMAN] [PP2AA_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2NYL
  • Community annotation for 2NYL 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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