3UMI	Metal Binding Protein	date	Nov 13, 2011
title	X-Ray Structure Of The E2 Domain Of The Human Amyloid Precur Protein (App) In Complex With Zinc
authors	S.O.Dahms, I.Konnig, D.Roeser, K.H.Guhrs, M.E.Than
compound		source
Molecule: Amyloid Beta A4 Protein Chain: A Fragment: Human Amyloid Precursor Protein E2 Domain Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet22b
symmetry	Space Group: P 43	R_factor 0.204 R_Free 0.245
crystal cell	length a length b length c angle alpha angle beta angle gamma 39.757 39.757 126.425 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.40 Å
ligand	ACT, CD, ZN	enzyme
Primary reference	Metal Binding Dictates Conformation and Function of the Amyloid Precursor Protein (APP) E2 Domain., Dahms SO, Konnig I, Roeser D, Guhrs KH, Mayer MC, Kaden D, Multhaup G, Than ME, J Mol Biol. 2012 Jan 4. PMID:22245578

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (39 Kb) [Save to disk] Biological Unit Coordinates (3umi.pdb1.gz) 34 Kb LPC: Ligand-Protein Contacts for 3UMI CSU: Contacts of Structural Units for 3UMI Structure Factors (52 Kb) Retrieve 3UMI in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3UMI from S2C, [Save to disk] Re-refined 3umi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3UMI 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3UMI

Cartoon representation from PDB Cartoon 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 Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 3UMI, from MSDmotif at EBI Fold representative 3umi from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3umi_A] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 3UMI with the sequences similar proteins can be viewed for 3UMI's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.

Other resources with information on 3UMI

Community annotation for 3UMI at PDBWiki (http://pdbwiki.org)

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Images from IMB Jena Image Library of Biological Macromolecules.

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