2YDX	Oxidoreductase	date	Mar 25, 2011
title	Crystal Structure Of Human S-Adenosylmethionine Synthetase 2 Subunit
authors	J.R.C.Muniz, N.Shafqat, A.C.W.Pike, W.W.Yue, M.Vollmar, V.Papagri A.Roos, O.Gileadi, F.Von Delft, K.L.Kavanagh, C.H.Arrowsmith, A.M.Edwards, J.Weigelt, C.Bountra, U.Oppermann
compound		source
Molecule: Methionine Adenosyltransferase 2 Subunit Beta Chain: A, B, C, D, E Fragment: Residues 28-335 Synonym: Dtdp-4-Keto-6-Deoxy-D-Glucose 4-Reductase, Methion Adenosyltransferase II Beta, Mat II Beta, S-Adenosylmethion Synthetase 2, Mat2b; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_variant: R3-Prare2 Expression_system_vector_type: Plasmid Expression_system_vector: Pnic-Cthf
symmetry	Space Group: P 42 21 2	R_factor 0.168 R_Free 0.188
crystal cell	length a length b length c angle alpha angle beta angle gamma 163.389 163.389 252.882 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	CA, NAP, SO4, STL, TXP	enzyme
Gene Ontology	Chain Function Process Component A, D, C, E, B methionine adenosyltransfera...
Primary reference	Insight into S-adenosylmethionine biosynthesis from the crystal structures of the human methionine adenosyltransferase catalytic and regulatory subunits., Shafqat N, Muniz JR, Pilka ES, Papagrigoriou E, von Delft F, Oppermann U, Yue WW, Biochem J. 2013 May 15;452(1):27-36. doi: 10.1042/BJ20121580. PMID:23425511

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (446 Kb) [Save to disk] Biological Unit Coordinates (2ydx.pdb1.gz) 221 Kb Biological Unit Coordinates (2ydx.pdb2.gz) 167 Kb Biological Unit Coordinates (2ydx.pdb3.gz) 162 Kb LPC: Ligand-Protein Contacts for 2YDX CSU: Contacts of Structural Units for 2YDX Structure Factors (4138 Kb) Retrieve 2YDX in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2YDX from S2C, [Save to disk] Re-refined 2ydx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2YDX 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 2YDX

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 2YDX, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2ydx_D] [2ydx_A] [2ydx] [2ydx_C] [2ydx_B] [2ydx_E] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 2YDX

Community annotation for 2YDX at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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