2XD1	Transferase	date	Apr 28, 2010
title	Active Site Restructuring Regulates Ligand Recognition In Cl Penicillin-Binding Proteins
authors	P.Macheboeuf, A.M.Di Guilmi, V.Job, T.Vernet, O.Dideberg, A.Desse
compound		source
Molecule: Penicillin-Binding Protein 1b Chain: A, B Fragment: Residues 101-125,323-791 Ec: 2.4.1.129, 2.3.2.- Engineered: Yes Mutation: Yes		Organism_scientific: Streptococcus Pneumoniae Organism_taxid: 171101 Strain: R6 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_plasmid: Pgex4t1
symmetry	Space Group: P 21 21 21	R_factor 0.161 R_Free 0.248
crystal cell	length a length b length c angle alpha angle beta angle gamma 96.600 102.300 146.500 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.00 Å
ligand	CEF, SO4	enzyme	Transferase E.C.2.4.1.129 BRENDA
note	2XD1 supersedes 2UWY, 2BG4
Gene Ontology	Chain Function Process Component A, B
Primary reference	Active site restructuring regulates ligand recognition in class A penicillin-binding proteins., Macheboeuf P, Di Guilmi AM, Job V, Vernet T, Dideberg O, Dessen A, Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):577-82. Epub 2005 Jan 6. PMID:15637155

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (152 Kb) [Save to disk] Biological Unit Coordinates (2xd1.pdb1.gz) 75 Kb Biological Unit Coordinates (2xd1.pdb2.gz) 72 Kb LPC: Ligand-Protein Contacts for 2XD1 CSU: Contacts of Structural Units for 2XD1 Structure Factors (227 Kb) Retrieve 2XD1 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2XD1 from S2C, [Save to disk] Re-refined 2xd1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2XD1 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 2XD1

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 2XD1, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2xd1_A] [2xd1_B] [2xd1] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 2XD1

Community annotation for 2XD1 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

---