3H6N	Signaling Protein	date	Apr 23, 2009
title	Crystal Structure Of The Ubiquitin-Like Domain Of Plexin D1
authors	Y.Tong, L.Nedyalkova, W.Tempel, F.Mackenzie, C.H.Arrowsmith, A.M. C.Bountra, J.Weigelt, A.Bochkarev, M.Buck, H.Park, Structural Ge Consortium (Sgc)
compound		source
Molecule: Plexin-D1 Chain: A Fragment: Ubiquitin-Like Domain (Unp Residues 1553-1678) Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Plxnd1, Kiaa0620 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3)-V2r-Prare2 Expression_system_plasmid: Pet28-Mhl
symmetry	Space Group: C 1 2 1	R_factor 0.243 R_Free 0.276
crystal cell	length a length b length c angle alpha angle beta angle gamma 81.777 27.051 52.653 90.00 114.06 90.00
method	X-Ray Diffraction	resolution	2.00 Å
ligand	ARS, MSE, UNX	enzyme
note	3H6N is a representative structure
Gene Ontology	Chain Function Process Component A

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (38 Kb) [Save to disk] Biological Unit Coordinates (3h6n.pdb1.gz) 66 Kb LPC: Ligand-Protein Contacts for 3H6N CSU: Contacts of Structural Units for 3H6N Likely Quarternary Molecular Structure file(s) for 3H6N Structure Factors (104 Kb) Retrieve 3H6N in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3H6N from S2C, [Save to disk] Re-refined 3h6n structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3H6N 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 3H6N

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 3H6N, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3h6n] [3h6n_A] SWISS-PROT database: [Q9Y4D7] Domain organization of [PLXD1_HUMAN] by SWISSPFAM

Other resources with information on 3H6N

Community annotation for 3H6N at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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