OCA Atlas for 5DFV

5DFV

Immune System

date

Aug 27, 2015

title

Crystal Structure Of Human Cd81 Large Extracellular Loop In With Murine Fab Fragment K04

authors

S.F.Harris, A.Wong, A.Kuglstatter

compound

source

Molecule: Cd81 Antigen
Chain: A, B
Synonym: 26 Kda Cell Surface Protein Tapa-1,Target Of The Antiproliferative Antibody 1,Tetraspanin-28,Tspan-28;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd81, Tapa1, Tspan28
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Fab Heavy Chain
Chain: C, E

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Cell_line: Murine Hybridoma

Molecule: Fab Light Chain
Chain: D, F

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Cell_line: Murine Hybridoma

symmetry

Space Group: P 1 21 1

R_factor

0.239

R_Free

0.291

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
77.631	94.483	94.114	90.00	104.14	90.00

method

X-Ray Diffraction

resolution

2.80 Å

Gene
Ontology

Chain	Function	Process	Component
A, B

Primary reference

VH-VL orientation prediction for antibody humanization candidate selection: A case study., Bujotzek A, Lipsmeier F, Harris SF, Benz J, Kuglstatter A, Georges G, MAbs. 2015 Dec 4:0. PMID:26637054

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (164 Kb) [Save to disk]

Biological Unit Coordinates (5dfv.pdb1.gz) 158 Kb

CSU: Contacts of Structural Units for 5DFV

Structure Factors (805 Kb)

Retrieve 5DFV in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 5DFV from S2C, [Save to disk]

Re-refined 5dfv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5DFV 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 5DFV

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5dfv_C] [5dfv_B] [5dfv_D] [5dfv] [5dfv_E] [5dfv_F] [5dfv_A]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Domains found in 5DFV: [IG_like] [IGv ] by SMART

Other resources with information on 5DFV

Community annotation for 5DFV at PDBWiki (http://pdbwiki.org)

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