5D62	Hydrolase	date	Aug 11, 2015
title	Moa-Z-Vad-Fmk Complex, Inverted Orientation
authors	G.Cordara, U.Krengel
compound		source
Molecule: Agglutinin Chain: A Engineered: Yes		Organism_scientific: Marasmius Oreades Organism_taxid: 181124 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pt7-Lo
Molecule: Z-Vad-Fmk Chain: L Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
symmetry	Space Group: P 63 2 2	R_factor 0.169 R_Free 0.198
crystal cell	length a length b length c angle alpha angle beta angle gamma 120.998 120.998 99.957 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.70 Å
ligand	CA, CF0, CL, DMS, EDO, FUC, GAL, GLA, PHQ	enzyme
Gene Ontology	Chain Function Process Component A
Primary reference	An Unusual Member of the Papain Superfamily: Mapping the Catalytic Cleft of the Marasmius oreades agglutinin (MOA) with a Caspase Inhibitor., Cordara G, van Eerde A, Grahn EM, Winter HC, Goldstein IJ, Krengel U, PLoS One. 2016 Feb 22;11(2):e0149407. doi: 10.1371/journal.pone.0149407., eCollection 2016. PMID:26901797

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (61 Kb) [Save to disk] Biological Unit Coordinates (5d62.pdb1.gz) 108 Kb LPC: Ligand-Protein Contacts for 5D62 CSU: Contacts of Structural Units for 5D62 Structure Factors (850 Kb) Retrieve 5D62 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5D62 from S2C, [Save to disk] Re-refined 5d62 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5D62 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 5D62

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5d62_L] [5d62] [5d62_A] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 5D62

Community annotation for 5D62 at PDBWiki (http://pdbwiki.org)

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