1QKM	Nuclear Receptor	date	Jul 27, 1999
title	Human Oestrogen Receptor Beta Ligand-Binding Domain In Complex With Partial Agonist Genistein
authors	A.C.W.Pike, A.M.Brzozowski, M.Carlquist
compound		source
Molecule: Estrogen Receptor Beta Chain: A Fragment: Ligand-Binding Domain Synonym: Oestrogen Receptor, Er-Lbd Engineered: Yes Other_details: Complexed With The Phyto-Oestrogen Genistein		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Oestrogen Receptor Beta Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Gi724 Expression_system_plasmid: Plex
symmetry	Space Group: P 61 2 2	R_factor 0.215 R_Free 0.252
crystal cell	length a length b length c angle alpha angle beta angle gamma 63.120 63.120 250.230 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.8 Å
ligand	GEN BindingDB	enzyme
related structures	by homologous chain: 1FM9
Primary reference	Structure of the ligand-binding domain of oestrogen receptor beta in the presence of a partial agonist and a full antagonist., Pike AC, Brzozowski AM, Hubbard RE, Bonn T, Thorsell AG, Engstrom O, Ljunggren J, Gustafsson JA, Carlquist M, EMBO J 1999 Sep 1;18(17):4608-18. PMID:10469641

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (46 Kb) [Save to disk] Biological Unit Coordinates (1qkm.pdb1.gz) 81 Kb LPC: Ligand-Protein Contacts for 1QKM CSU: Contacts of Structural Units for 1QKM Likely Quarternary Molecular Structure file(s) for 1QKM Structure Factors (197 Kb) Retrieve 1QKM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1QKM from S2C, [Save to disk] Re-refined 1qkm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1QKM 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 1QKM

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 1QKM, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1qkma_, region A [Jmol] [rasmolscript] [script source] Fold representative 1qkm from FSSP and Dali (Families of Structurally Similar Proteins) Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1qkm_A] SWISS-PROT database: [Q92731] Domain organization of [ESR2_HUMAN] by SWISSPFAM Domain found in 1QKM: [HOLI ] by SMART Alignments of the sequence of 1QKM with the sequences similar proteins can be viewed for 1QKM's classification [ESR2_HUMAN] 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 [ESR2_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 1QKM

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

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