2BEF	Phosphotransferase	date	May 26, 1998
title	Crystal Structure Of Ndp Kinase Complexed With Mg, Adp, And
authors	Y.W.Xu, J.Cherfils
compound		source
Molecule: Nucleoside Diphosphate Kinase Chain: A, B, C Ec: 2.7.4.6 Engineered: Yes Other_details: Adp, Bef3, Mg++		Organism_scientific: Dictyostelium Discoideum Organism_taxid: 44689 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 31 2 1	R_factor 0.193 R_Free NULL
crystal cell	length a length b length c angle alpha angle beta angle gamma 71.560 71.560 153.750 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	ADP, BEF, MG	enzyme	Transferase E.C.2.7.4.6 BRENDA
related structures	by homologous chain: 1JXV, 1ZS6
Gene Ontology	Chain Function Process Component A, C, B
Primary reference	AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP., Xu YW, Morera S, Janin J, Cherfils J, Proc Natl Acad Sci U S A 1997 Apr 15;94(8):3579-83. PMID:9108019

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (82 Kb) [Save to disk] Biological Unit Coordinates (2bef.pdb1.gz) 152 Kb LPC: Ligand-Protein Contacts for 2BEF CSU: Contacts of Structural Units for 2BEF Likely Quarternary Molecular Structure file(s) for 2BEF Structure Factors (154 Kb) Retrieve 2BEF in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2BEF from S2C, [Save to disk] Re-refined 2bef structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2BEF 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 2BEF

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 3D motif for 2BEF, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d2befa_, region A [Jmol] [rasmolscript] [script source]     - Domain d2befb_, region B [Jmol] [rasmolscript] [script source]     - Domain d2befc_, region C [Jmol] [rasmolscript] [script source] 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: [2bef] [2bef_B] [2bef_A] [2bef_C] SWISS-PROT database: [P22887] Domain organization of [NDKC_DICDI] by SWISSPFAM Domain found in 2BEF: [NDK ] by SMART

Other resources with information on 2BEF

Community annotation for 2BEF at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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