1YMD	Hydrolase, Cell Cycle	date	Jan 20, 2005
title	Crystal Structure Of The Cdc25b Phosphatase Catalytic Domain Active Site Cysteine In The Sulfonic Form
authors	G.K.Buhrman, B.Parker, J.Sohn, J.Rudolph, C.Mattos
compound		source
Molecule: M-Phase Inducer Phosphatase 2 Chain: A Fragment: Catalytic Domain Synonym: Cdc25b Phosphatase; Dual Specificity Phosphatase C Ec: 3.1.3.48 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Cdc25b, Cdc25hu2 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 21 21 21	R_factor 0.188 R_Free 0.209
crystal cell	length a length b length c angle alpha angle beta angle gamma 49.702 71.152 74.431 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.70 Å
ligand	CL, OCS	enzyme	Hydrolase E.C.3.1.3.48 BRENDA
related structures	by homologous chain: 1YMK, 1YML
Gene Ontology	Chain Function Process Component A
Primary reference	Structural mechanism of oxidative regulation of the phosphatase Cdc25B via an intramolecular disulfide bond., Buhrman G, Parker B, Sohn J, Rudolph J, Mattos C, Biochemistry 2005 Apr 12;44(14):5307-16. PMID:15807524

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (37 Kb) [Save to disk] Biological Unit Coordinates (1ymd.pdb1.gz) 33 Kb LPC: Ligand-Protein Contacts for 1YMD CSU: Contacts of Structural Units for 1YMD Likely Quarternary Molecular Structure file(s) for 1YMD Structure Factors (232 Kb) Retrieve 1YMD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1YMD from S2C, [Save to disk] Re-refined 1ymd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1YMD 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 1YMD

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 1YMD, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ymd_A] [1ymd] SWISS-PROT database: [P30305] Domain organization of [MPIP2_HUMAN] by SWISSPFAM Domain found in 1YMD: [RHOD ] by SMART

Other resources with information on 1YMD

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

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