1X9D	Hydrolase	date	Aug 20, 2004
title	Crystal Structure Of Human Class I Alpha-1,2-Mannosidase In With Thio-Disaccharide Substrate Analogue
authors	K.Karaveg, W.Tempel, Z.J.Liu, A.Siriwardena, K.W.Moremen, B.C.Wan
compound		source
Molecule: Endoplasmic Reticulum Mannosyl-Oligosaccharide 1, Mannosidase; Chain: A Fragment: Residues 243-699 Synonym: Er Alpha-1,2-Mannosidase, Mannosidase Alpha Class 1, Man9glcnac2-Specific Processing Alpha-Mannosidase, Unq74 Ec: 3.2.1.113 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Man1b1 Expression_system: Pichia Pastoris Expression_system_taxid: 4922
symmetry	Space Group: P 1	R_factor 0.144 R_Free 0.162
crystal cell	length a length b length c angle alpha angle beta angle gamma 50.687 53.878 56.234 89.49 63.60 62.61
method	X-Ray Diffraction	resolution	1.41 Å
ligand	BU1, CA, MAN, SO4, Z5L	enzyme	Hydrolase E.C.3.2.1.113 BRENDA
note	1X9D is a representative structure
related structures	by homologous chain: 1FO3
Gene Ontology	Chain Function Process Component A
Primary reference	Mechanism of class 1 (glycosylhydrolase family 47) {alpha}-mannosidases involved in N-glycan processing and endoplasmic reticulum quality control., Karaveg K, Siriwardena A, Tempel W, Liu ZJ, Glushka J, Wang BC, Moremen KW, J Biol Chem 2005 Apr 22;280(16):16197-207. Epub 2005 Feb 15. PMID:15713668

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk] Biological Unit Coordinates (1x9d.pdb1.gz) 80 Kb LPC: Ligand-Protein Contacts for 1X9D CSU: Contacts of Structural Units for 1X9D Likely Quarternary Molecular Structure file(s) for 1X9D Structure Factors (581 Kb) Retrieve 1X9D in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1X9D from S2C, [Save to disk] Re-refined 1x9d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1X9D 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 1X9D

Ramachandran plot from PDBSum

Structure-derived information

Conformational Epitope Prediction for 1X9D 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 1X9D, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1x9d_A] [1x9d] SWISS-PROT database: [Q9UKM7] Domain organization of [MA1B1_HUMAN] by SWISSPFAM

Other resources with information on 1X9D

Community annotation for 1X9D at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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