3G3D	Lyase	date	Feb 02, 2009
title	Crystal Structure Of Human Orotidine 5'-Monophosphate Decarb Covalently Modified By 5-Fluoro-6-Azido-Ump
authors	Y.Liu, H.L.Tang, A.Bello, E.Poduch, L.Kotra, E.Pai
compound		source
Molecule: Uridine 5'-Monophosphate Synthase Chain: A, B Fragment: Unp Residues 190-480, Orotidine 5'-Phosphate Deca Domain; Synonym: Ump Synthase Ec: 4.1.1.23 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Gi|13960142, Oksw-Cl.21, Umps Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3)Plyss Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet15b
symmetry	Space Group: P 1 21 1	R_factor 0.175 R_Free 0.210
crystal cell	length a length b length c angle alpha angle beta angle gamma 69.682 61.850 70.320 90.00 112.73 90.00
method	X-Ray Diffraction	resolution	1.70 Å
ligand	5FU, GOL, SO4 BindingDB	enzyme	Lyase E.C.4.1.1.23 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Structure-activity relationships of orotidine-5'-monophosphate decarboxylase inhibitors as anticancer agents., Bello AM, Konforte D, Poduch E, Furlonger C, Wei L, Liu Y, Lewis M, Pai EF, Paige CJ, Kotra LP, J Med Chem. 2009 Mar 26;52(6):1648-58. PMID:19260677

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (97 Kb) [Save to disk] Biological Unit Coordinates (3g3d.pdb1.gz) 91 Kb LPC: Ligand-Protein Contacts for 3G3D CSU: Contacts of Structural Units for 3G3D Likely Quarternary Molecular Structure file(s) for 3G3D Structure Factors (436 Kb) Retrieve 3G3D in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3G3D from S2C, [Save to disk] Re-refined 3g3d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3G3D 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 3G3D

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 3G3D, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3g3d] [3g3d_B] [3g3d_A] SWISS-PROT database: [P11172] Domain organization of [PYR5_HUMAN] by SWISSPFAM Domain found in 3G3D: [OMPdecase ] by SMART

Other resources with information on 3G3D

Community annotation for 3G3D at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---