OCA Atlas for 3F12

3F12

Immune System

date

Oct 27, 2008

title

Germline V-Genes Sculpt The Binding Site Of A Family Of Anti Neutralizing Human Cytomegalovirus

authors

C.A.Thomson, S.Bryson, G.R.Mclean, A.L.Creagh, E.F.Pai, J.W.Schra

compound

source

Molecule: M2j1 Fab
Chain: A, C
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet32b

Molecule: 8f9 Fab
Chain: B, D
Engineered: Yes

symmetry

Space Group: P 32 2 1

R_factor

0.300

R_Free

0.320

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
87.860	87.860	241.850	90.00	90.00	120.00

method

X-Ray Diffraction

resolution

2.95 Å

Primary reference

Germline V-genes sculpt the binding site of a family of antibodies neutralizing human cytomegalovirus., Thomson CA, Bryson S, McLean GR, Creagh AL, Pai EF, Schrader JW, EMBO J. 2008 Oct 8;27(19):2592-602. Epub 2008 Sep 4. PMID:18772881

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (131 Kb) [Save to disk]

Biological Unit Coordinates (3f12.pdb1.gz) 64 Kb

Biological Unit Coordinates (3f12.pdb2.gz) 65 Kb

CSU: Contacts of Structural Units for 3F12

Structure Factors (436 Kb)

Retrieve 3F12 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3F12 from S2C, [Save to disk]

Re-refined 3f12 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3F12 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 3F12

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 3F12, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3f12_A] [3f12_C] [3f12_B] [3f12_D] [3f12]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Domains found in 3F12: [IG_like] [IGv ] by SMART

Other resources with information on 3F12

Community annotation for 3F12 at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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