OCA Atlas for 2KZT

2KZT

Apoptosis

date

Jun 24, 2010

title

Structure Of The Tandem Ma-3 Region Of Pdcd4

authors

L.C.Waters, S.L.Strong, O.Oka, F.W.Muskett, V.Veverka, S.Banerjee T.Schmedt, A.J.Henry, K.H.Klempnauer, M.D.Carr

compound

source

Molecule: Programmed Cell Death Protein 4
Chain: A
Fragment: Ma-3 Region, Residues 157-318
Synonym: Pdcd4, Nuclear Antigen H731-Like, Neoplastic Trans Inhibitor Protein, Protein 19715a;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Vector
Expression_system_vector: Pgex-6p-2

Molecule: Programmed Cell Death Protein 4
Chain: B
Fragment: Ma-3 Region, Residues 319-449
Synonym: Pdcd4, Topoisomerase-Inhibitor Suppressed Protein, Ma-3;
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Vector
Expression_system_vector: Pgex-6p-2

method

Solution NMR

Gene
Ontology

Chain	Function	Process	Component
A, B

Primary reference

Structure of the tandem MA-3 region of Pdcd4 protein and characterization of its interactions with eIF4A and eIF4G: molecular mechanisms of a tumor suppressor., Waters LC, Strong SL, Ferlemann E, Oka O, Muskett FW, Veverka V, Banerjee S, Schmedt T, Henry AJ, Klempnauer KH, Carr MD, J Biol Chem. 2011 May 13;286(19):17270-80. Epub 2011 Mar 16. PMID:21454508

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3437 Kb) [Save to disk]

Biological Unit Coordinates (2kzt.pdb1.gz) 48 Kb

CSU: Contacts of Structural Units for 2KZT

Original NMR restraints for 2KZT from PDB

Retrieve 2KZT in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 2KZT from S2C, [Save to disk]

View 2KZT 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 2KZT

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 2KZT, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2kzt_B] [2kzt_A] [2kzt]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Domain found in 2KZT: [MA3 ] by SMART

Other resources with information on 2KZT

Community annotation for 2KZT 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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