5DMI	Immune System Signaling Protein	date	Sep 08, 2015
title	Structure Of The Extracellular Domain Of The Cd40 In Complex Chi220 Fab
authors	S.Sheriff
compound		source
Molecule: Tumor Necrosis Factor Receptor Superfamily Member Chain: A Fragment: Extracellular Domain Residues 23-193 Synonym: B-Cell Surface Antigen Cd40,Bp50,Cd40l Receptor,Cd Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Cd40, Tnfrsf5 Expression_system: Homo Sapiens Expression_system_common: Human Expression_system_taxid: 9606 Expression_system_cell_line: Hek293
Molecule: Chi220 Fab Heavy Chain Chain: H Engineered: Yes		Organism_scientific: Mus Musculus, Homo Sapiens Organism_taxid: 10090, 9606 Expression_system: Cricetulus Griseus Expression_system_common: Chinese Hamster Expression_system_taxid: 10029
Molecule: Chi220 Fab Light Chain Chain: L Engineered: Yes		Organism_scientific: Mus Musculus, Homo Sapiens Organism_taxid: 10090, 9606 Expression_system: Cricetulus Griseus Expression_system_common: Chinese Hamster Expression_system_taxid: 10029
symmetry	Space Group: P 42 21 2	R_factor 0.168 R_Free 0.207
crystal cell	length a length b length c angle alpha angle beta angle gamma 201.152 201.152 63.809 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.69 Å
ligand	SO4	enzyme
Gene Ontology	Chain Function Process Component A
Primary reference	Functional antagonism of human CD40 achieved by targeting a unique species-specific epitope., Yamniuk AP, Suri A, Krystek SR, Tamura J, Ramamurthy V, Kuhn R, Carroll K, Fleener C, Ryseck R, Cheng L, An Y, Drew P, Grant S, Suchard SJ, Nadler SG, Bryson JW, Sheriff S, J Mol Biol. 2016 May 21. pii: S0022-2836(16)30169-3. doi:, 10.1016/j.jmb.2016.05.014. PMID:27216500

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (88 Kb) [Save to disk] Biological Unit Coordinates (5dmi.pdb1.gz) 82 Kb LPC: Ligand-Protein Contacts for 5DMI CSU: Contacts of Structural Units for 5DMI Structure Factors (883 Kb) Retrieve 5DMI in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5DMI from S2C, [Save to disk] Re-refined 5dmi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5DMI 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 5DMI

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: [5dmi_A] [5dmi] [5dmi_L] [5dmi_H] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 5DMI: [IG_like] [IGv] [TNFR ] by SMART

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