1NPD	Structural Genomics, Unknown Function	date	Jan 17, 2003
title	X-Ray Structure Of Shikimate Dehydrogenase Complexed With Na E.Coli (Ydib) Northeast Structural Genomics Research Consor (Nesg) Target Er24
authors	J.Benach, A.P.Kuzin, I.Lee, B.Rost, Y.Chiang, T.B.Acton, G.T.Monte J.F.Hunt, Northeast Structural Genomics Consortium (Nesg)
compound		source
Molecule: Hypothetical Shikimate 5-Dehydrogenase-Like Prote Chain: A, B Ec: 1.1.1.25 Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 562 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21 (De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pmgk
symmetry	Space Group: P 64	R_factor 0.217 R_Free 0.274
crystal cell	length a length b length c angle alpha angle beta angle gamma 157.185 157.185 39.782 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	MSE, NAD	enzyme	Oxidoreductase E.C.1.1.1.25 BRENDA
related structures	by homologous chain: 1O9B, 1VI2
Gene Ontology	Chain Function Process Component A, B
Primary reference	The 2.3-A crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase., Benach J, Lee I, Edstrom W, Kuzin AP, Chiang Y, Acton TB, Montelione GT, Hunt JF, J Biol Chem 2003 May 23;278(21):19176-82. PMID:12624088

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (104 Kb) [Save to disk] Biological Unit Coordinates (1npd.pdb1.gz) 98 Kb LPC: Ligand-Protein Contacts for 1NPD CSU: Contacts of Structural Units for 1NPD Likely Quarternary Molecular Structure file(s) for 1NPD Structure Factors (206 Kb) Retrieve 1NPD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1NPD from S2C, [Save to disk] Re-refined 1npd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1NPD 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 1NPD

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 1NPD, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1npda2, region A:1-106 [Jmol] [rasmolscript] [script source]     - Domain d1npda1, region A:107-287 [Jmol] [rasmolscript] [script source]     - Domain d1npdb2, region B:1-106 [Jmol] [rasmolscript] [script source]     - Domain d1npdb1, region B:107-288 [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: [1npd_B] [1npd_A] [1npd] SWISS-PROT database: [P0A6D5] Domain organization of [YDIB_ECOLI] by SWISSPFAM

Other resources with information on 1NPD

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

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