5TSW	Lymphokine	date	Apr 22, 1999
title	High Resolution Crystal Structure Of A Human Tnf-Alpha Mutant
authors	S.S.Cha, J.S.Kim, H.S.Cho, B.H.Oh
compound		source
Molecule: Protein (Tumor Necrosis Factor-Alpha) Chain: A, B, C, D, E, F Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21 (De3)
symmetry	Space Group: P 21 21 21	R_factor 0.207 R_Free 0.299
crystal cell	length a length b length c angle alpha angle beta angle gamma 94.170 94.560 95.890 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.50 Å
note	5TSW supersedes 4TSW
related structures	by homologous chain: 1A8M, 1TNF
Primary reference	High resolution crystal structure of a human tumor necrosis factor-alpha mutant with low systemic toxicity., Cha SS, Kim JS, Cho HS, Shin NK, Jeong W, Shin HC, Kim YJ, Hahn JH, Oh BH, J Biol Chem 1998 Jan 23;273(4):2153-60. PMID:9442056

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (187 Kb) [Save to disk] Biological Unit Coordinates (5tsw.pdb1.gz) 91 Kb Biological Unit Coordinates (5tsw.pdb2.gz) 92 Kb CSU: Contacts of Structural Units for 5TSW Likely Quarternary Molecular Structure file(s) for 5TSW Structure Factors (313 Kb) Retrieve 5TSW in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5TSW from S2C, [Save to disk] Re-refined 5tsw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5TSW 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 5TSW

Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 5TSW, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d5tswa_, region A [Jmol] [rasmolscript] [script source]     - Domain d5tswb_, region B [Jmol] [rasmolscript] [script source]     - Domain d5tswc_, region C [Jmol] [rasmolscript] [script source]     - Domain d5tswd_, region D [Jmol] [rasmolscript] [script source]     - Domain d5tswe_, region E [Jmol] [rasmolscript] [script source]     - Domain d5tswf_, region F [Jmol] [rasmolscript] [script source] Fold representative 5tsw 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: [5tsw_A] [5tsw_B] [5tsw_C] [5tsw_D] [5tsw_E] [5tsw_F] SWISS-PROT database: [P01375] Domain organization of [TNFA_HUMAN] by SWISSPFAM Domain found in 5TSW: [TNF ] by SMART Alignments of the sequence of 5TSW with the sequences similar proteins can be viewed for 5TSW's classification [TNFA_HUMAN] 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 [TNFA_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 5TSW

Community annotation for 5TSW at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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