3VBB	Ligase	date	Jan 02, 2012
title	Crystal Structure Of Seryl-Trna Synthetase From Human At 2.9
authors	X.L.Xu, X.L.Yang
compound		source
Molecule: Seryl-Trna Synthetase, Cytoplasmic Chain: A, B, C, D, E, F Synonym: Serine--Trna Ligase, Serrs, Seryl-Trna(Sersec) Sy Ec: 6.1.1.11 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Sars, Sers Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: E.Coli Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet20b
symmetry	Space Group: P 21 21 21	R_factor 0.194 R_Free 0.250
crystal cell	length a length b length c angle alpha angle beta angle gamma 116.800 189.417 230.589 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.89 Å
ligand	MG, PO4	enzyme	Ligase E.C.6.1.1.11 BRENDA
Gene Ontology	Chain Function Process Component F, A, D, C, E, B
Primary reference	Unique domain appended to vertebrate tRNA synthetase is essential for vascular development., Xu X, Shi Y, Zhang HM, Swindell EC, Marshall AG, Guo M, Kishi S, Yang XL, Nat Commun. 2012 Feb 21;3:681. doi: 10.1038/ncomms1686. PMID:22353712

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (436 Kb) [Save to disk] Biological Unit Coordinates (3vbb.pdb1.gz) 149 Kb Biological Unit Coordinates (3vbb.pdb2.gz) 147 Kb Biological Unit Coordinates (3vbb.pdb3.gz) 144 Kb LPC: Ligand-Protein Contacts for 3VBB CSU: Contacts of Structural Units for 3VBB Structure Factors (1459 Kb) Retrieve 3VBB in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3VBB from S2C, [Save to disk] Re-refined 3vbb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3VBB 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 3VBB

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 3VBB, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3vbb] [3vbb_A] [3vbb_C] [3vbb_D] [3vbb_F] [3vbb_E] [3vbb_B] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 3VBB

Community annotation for 3VBB at PDBWiki (http://pdbwiki.org)

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

---