1T5W	Immune System	date	May 05, 2004
title	Hla-Dr1 In Complex With A Synthetic Peptide (Aaysdqatplllspr)
authors	Z.Zavala-Ruiz, I.Strug, M.W.Anderson, J.Gorski, L.J.Stern
compound		source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha Chain; Chain: A, D Fragment: Extracellular Domain Synonym: Mhc Class II Antigen Dra Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Hla-Dra Expression_system: Drosophila Melanogaster Expression_system_common: Fruit Fly Expression_system_taxid: 7227 Expression_system_cell_line: S2 Expression_system_vector_type: Plasmid Expression_system_plasmid: Prmaha-3
Molecule: Hla Class II Histocompatibility Antigen, Drb1-1 Beta Chain; Chain: B, E Fragment: Extracellular Domain Synonym: Mhc Class I Antigen Drb11, Dr-1, Dr1 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Hla-Drb1 Expression_system: Drosophila Melanogaster Expression_system_common: Fruit Fly Expression_system_taxid: 7227 Expression_system_cell_line: S2 Expression_system_vector_type: Plasmid Expression_system_plasmid: Prmha-3
Molecule: 15-Mer Peptide Fragment Of Regulatory Protein Mig1; Chain: C, F Fragment: Synthetic Peptide Synonym: Regulatory Protein Cat4 Engineered: Yes		Synthetic: Yes Other_details: Synthetic Peptide Desinged To Study The P10 Side Chain Specificity Of Hla-Dr1
symmetry	Space Group: C 2 2 21	R_factor 0.231 R_Free 0.255
crystal cell	length a length b length c angle alpha angle beta angle gamma 96.554 112.646 206.976 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.40 Å
related structures	by homologous chain: 1I3R, 1SJE, 2IAD
Primary reference	A polymorphic pocket at the P10 position contributes to peptide binding specificity in class II MHC proteins., Zavala-Ruiz Z, Strug I, Anderson MW, Gorski J, Stern LJ, Chem Biol 2004 Oct;11(10):1395-402. PMID:15489166

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (134 Kb) [Save to disk] Biological Unit Coordinates (1t5w.pdb1.gz) 67 Kb Biological Unit Coordinates (1t5w.pdb2.gz) 65 Kb CSU: Contacts of Structural Units for 1T5W Likely Quarternary Molecular Structure file(s) for 1T5W Structure Factors (427 Kb) Retrieve 1T5W in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1T5W from S2C, [Save to disk] Re-refined 1t5w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1T5W 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 1T5W

Cartoon representation from PDB Cartoon 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 Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 1T5W, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1t5wa2, region A:4-81 [Jmol] [rasmolscript] [script source]     - Domain d1t5wa1, region A:82-181 [Jmol] [rasmolscript] [script source]     - Domain d1t5wb2, region B:1-92 [Jmol] [rasmolscript] [script source]     - Domain d1t5wb1, region B:93-190 [Jmol] [rasmolscript] [script source]     - Domain d1t5wd2, region D:4-81 [Jmol] [rasmolscript] [script source]     - Domain d1t5wd1, region D:82-181 [Jmol] [rasmolscript] [script source]     - Domain d1t5we2, region E:1-92 [Jmol] [rasmolscript] [script source]     - Domain d1t5we1, region E:93-190 [Jmol] [rasmolscript] [script source] Fold representative 1t5w from FSSP and Dali (Families of Structurally Similar Proteins) Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1t5w_A] [1t5w_B] [1t5w_C] [1t5w_D] [1t5w_E] [1t5w_F] SWISS-PROT database: [P04229] [P01903] [P27705] Domain organization of [2B11_HUMAN] [DRA_HUMAN] [MIG1_YEAST] by SWISSPFAM Domains found in 1T5W: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART Alignments of the sequence of 1T5W with the sequences similar proteins can be viewed for 1T5W's classification [2B11_HUMAN] [DRA_HUMAN] [MIG1_YEAST] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [2B11_HUMAN] [DRA_HUMAN] [MIG1_YEAST] at ProtoMap. Click on the Cluster number.

Other resources with information on 1T5W

Community annotation for 1T5W at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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