1KDN	Phosphotransferase	date	Sep 10, 1996
title	Structure Of Nucleoside Diphosphate Kinase
authors	J.Cherfils, Y.W.Xu, S.Morera, J.Janin
compound		source
Molecule: Nucleoside Diphosphate Kinase Chain: A, B, C Ec: 2.7.4.6 Engineered: Yes		Organism_scientific: Dictyostelium Discoideum Organism_taxid: 44689 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 31 2 1	R_factor 0.177 R_Free 0.179
crystal cell	length a length b length c angle alpha angle beta angle gamma 71.354 71.354 153.494 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.00 Å
ligand	ADP, AF3, MG	enzyme	Transferase E.C.2.7.4.6 BRENDA
related structures	by homologous chain: 1F6T, 1NUE
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] (83 Kb) [Save to disk] Biological Unit Coordinates (1kdn.pdb1.gz) 152 Kb LPC: Ligand-Protein Contacts for 1KDN CSU: Contacts of Structural Units for 1KDN Likely Quarternary Molecular Structure file(s) for 1KDN Structure Factors (223 Kb) Retrieve 1KDN in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1KDN from S2C, [Save to disk] Re-refined 1kdn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1KDN 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 1KDN

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 1KDN, from MSDmotif at EBI Genome occurence of 1KDN's fold from GeneCensus Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1kdna_, region A [Jmol] [rasmolscript] [script source]     - Domain d1kdnb_, region B [Jmol] [rasmolscript] [script source]     - Domain d1kdnc_, 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: [1kdn] [1kdn_C] [1kdn_A] [1kdn_B] SWISS-PROT database: [P22887] Domain organization of [NDKC_DICDI] by SWISSPFAM Domain found in 1KDN: [NDK ] by SMART

Other resources with information on 1KDN

Community annotation for 1KDN at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---