1WDD	Lyase	date	May 13, 2004
title	Crystal Structure Of Activated Rice Rubisco Complexed With 2 Carboxyarabinitol-1,5-Bisphosphate
authors	E.Mizohata, H.Matsumura, T.Ueno, H.Ishida, T.Inoue, A.Makino, T.Ma
compound		source
Molecule: Ribulose Bisphosphate Carboxylase Large Chain Chain: A, E Synonym: Large Subunit Of Ribulose-1,5-Bisphosphate Carboxylaseoxygenase, Rubisco Large Subunit; Ec: 4.1.1.39		Organism_scientific: Oryza Sativa Japonica Group Organism_common: Japanese Rice Organism_taxid: 39947 Tissue: Leaves
Molecule: Ribulose Bisphosphate Carboxylase Small Chain C Chain: S, W Synonym: Small Subunit Of Ribulose-1,5-Bisphosphate Carboxylaseoxygenase, Rubisco Small Subunit C; Ec: 4.1.1.39		Organism_scientific: Oryza Sativa Japonica Group Organism_common: Japanese Rice Organism_taxid: 39947 Tissue: Leaves
symmetry	Space Group: I 4	R_factor 0.160 R_Free 0.182
crystal cell	length a length b length c angle alpha angle beta angle gamma 111.713 111.713 196.780 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.35 Å
ligand	CAP, GOL, KCX, MG, MME	enzyme	Lyase E.C.4.1.1.39 BRENDA
related structures	by homologous chain: 1GK8, 8RUC
Gene Ontology	Chain Function Process Component A, E
Primary reference	Crystal Structure of Rice Rubisco and Implications for Activation Induced by Positive Effectors NADPH and 6-Phosphogluconate., Matsumura H, Mizohata E, Ishida H, Kogami A, Ueno T, Makino A, Inoue T, Yokota A, Mae T, Kai Y, J Mol Biol. 2012 May 17. PMID:22609438

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (212 Kb) [Save to disk] Biological Unit Coordinates (1wdd.pdb1.gz) 809 Kb LPC: Ligand-Protein Contacts for 1WDD CSU: Contacts of Structural Units for 1WDD Likely Quarternary Molecular Structure file(s) for 1WDD Structure Factors (2165 Kb) Retrieve 1WDD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1WDD from S2C, [Save to disk] Re-refined 1wdd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1WDD 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 1WDD

Ramachandran plot from PDBSum

Structure-derived information

Conformational Epitope Prediction for 1WDD 1WDDA 1WDDE 1WDDS 1WDDW from the CEP Server. Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1WDD, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1wdda2, region A:11-150 [Jmol] [rasmolscript] [script source]     - Domain d1wdda1, region A:151-475 [Jmol] [rasmolscript] [script source]     - Domain d1wdde2, region E:12-150 [Jmol] [rasmolscript] [script source]     - Domain d1wdde1, region E:151-475 [Jmol] [rasmolscript] [script source]     - Domain d1wdds_, region S [Jmol] [rasmolscript] [script source]     - Domain d1wddw_, region W [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1wdd_W] [1wdd_A] [1wdd] [1wdd_S] [1wdd_E] SWISS-PROT database: [P0C512] [Q0INY7] Domain organization of [RBL_ORYSJ] [RBS1_ORYSJ] by SWISSPFAM Domain found in 1WDD: [RuBisCO_small ] by SMART

Other resources with information on 1WDD

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

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