5HDB	Membrane Protein Immune System	date	Jan 05, 2016
title	Integrin Alphaiibbeta3 In Complex With Ro-435054
authors	F.Y.Lin
compound		source
Molecule: Integrin Alpha-Iib Chain: A, C Synonym: Gpalpha Iib,Gpiib,Platelet Membrane Glycoprotein I Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Itga2b, Gp2b, Itgab Expression_system: Cricetulus Griseus Expression_system_taxid: 10029
Molecule: Integrin Beta-3 Chain: B, D Synonym: Platelet Membrane Glycoprotein Iiia,Gpiiia Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Itgb3, Gp3a Expression_system: Cricetulus Griseus Expression_system_taxid: 10029
Molecule: Monoclonal Antibody 10e5 Heavy Chain Chain: E, H Engineered: Yes		Organism_scientific: Mus Musculus Organism_taxid: 10090 Expression_system: Cricetulus Griseus Expression_system_taxid: 10029
Molecule: Monoclonal Antibody 10e5 Light Chain Chain: F, L Engineered: Yes		Organism_scientific: Mus Musculus Organism_taxid: 10090 Expression_system: Cricetulus Griseus Expression_system_taxid: 10029
symmetry	Space Group: P 21 21 2	R_factor 0.212 R_Free 0.238
crystal cell	length a length b length c angle alpha angle beta angle gamma 259.346 144.439 104.901 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.70 Å
ligand	5YB, BMA, CA, CL, GOL, MAN, MG, NAG, SO4	enzyme
note	5HDB supersedes 4Z7S
Gene Ontology	Chain Function Process Component A, C D, B
Primary reference	beta-subunit Binding is Sufficient for Ligands to open the Integrin alphaIIbbeta3 Headpiece., Lin FY, Zhu J, Eng ET, Hudson NE, Springer TA, J Biol Chem. 2015 Dec 2. pii: jbc.M115.705624. PMID:26631735

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1315 Kb) [Save to disk] Biological Unit Coordinates (5hdb.pdb1.gz) 454 Kb Biological Unit Coordinates (5hdb.pdb2.gz) 451 Kb Biological Unit Coordinates (5hdb.pdb3.gz) 209 Kb Biological Unit Coordinates (5hdb.pdb4.gz) 210 Kb LPC: Ligand-Protein Contacts for 5HDB CSU: Contacts of Structural Units for 5HDB Structure Factors (711 Kb) Retrieve 5HDB in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5HDB from S2C, [Save to disk] Re-refined 5hdb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5HDB 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 5HDB

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: [5hdb_H] [5hdb] [5hdb_E] [5hdb_C] [5hdb_B] [5hdb_L] [5hdb_A] [5hdb_F] [5hdb_D] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 5HDB: [IG_like] [IGv] [INB] [Int_alpha] [PSI] [VWA ] by SMART

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