3H5K	Hydrolase	date	Apr 22, 2009
title	Crystal Structure Of The Ribosome Inactivating Protein Pdl1
authors	A.Ruggiero, A.Di Maro, V.Severino, A.Chambery, R.Berisio
compound		source
Molecule: Ribosome-Inactivating Protein Pd-L1pd-L2 Chain: A, B Synonym: Rrna N-Glycosidase Pd-L1pd-L2 Ec: 3.2.2.22		Organism_scientific: Phytolacca Dioica Organism_common: Bella Sombra Tree Organism_taxid: 29725
symmetry	Space Group: C 1 2 1	R_factor 0.196 R_Free 0.242
crystal cell	length a length b length c angle alpha angle beta angle gamma 161.011 34.735 120.630 90.00 127.99 90.00
method	X-Ray Diffraction	resolution	1.45 Å
ligand	EDO, NAG	enzyme	Hydrolase E.C.3.2.2.22 BRENDA
Gene Ontology	Chain Function Process Component A, B toxin activity
Primary reference	Crystal structure of PD-L1, a ribosome inactivating protein from Phytolacca dioica L. Leaves with the property to induce DNA cleavage., Ruggiero A, Di Maro A, Severino V, Chambery A, Berisio R, Biopolymers. 2009 May 18;91(12):1135-1142. PMID:19452522

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (103 Kb) [Save to disk] Biological Unit Coordinates (3h5k.pdb1.gz) 50 Kb Biological Unit Coordinates (3h5k.pdb2.gz) 50 Kb LPC: Ligand-Protein Contacts for 3H5K CSU: Contacts of Structural Units for 3H5K Structure Factors (2456 Kb) Retrieve 3H5K in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3H5K from S2C, [Save to disk] Re-refined 3h5k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3H5K 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 3H5K

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 3H5K, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3h5k] [3h5k_B] [3h5k_A] SWISS-PROT database: [P84853] Domain organization of [RIPL1_PHYDI] by SWISSPFAM

Other resources with information on 3H5K

Community annotation for 3H5K at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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