1A8M	Lymphokine	date	Mar 27, 1998
title	Tumor Necrosis Factor Alpha, R31d Mutant
authors	C.Reed, Z.Q.Fu, J.Wu, Y.N.Xue, R.W.Harrison, M.J.Chen, I.T.Weber
compound		source
Molecule: Tumor Necrosis Factor Alpha Chain: A, B, C Synonym: Tnf-Alpha Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 41 21 2	R_factor 0.218 R_Free 0.240
crystal cell	length a length b length c angle alpha angle beta angle gamma 94.700 94.700 117.400 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.30 Å
related structures	by homologous chain: 4TSV, 5TSW
Primary reference	Crystal structure of TNF-alpha mutant R31D with greater affinity for receptor R1 compared with R2., Reed C, Fu ZQ, Wu J, Xue YN, Harrison RW, Chen MJ, Weber IT, Protein Eng 1997 Oct;10(10):1101-7. PMID:9488135

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk] Biological Unit Coordinates (1a8m.pdb1.gz) 74 Kb CSU: Contacts of Structural Units for 1A8M Likely Quarternary Molecular Structure file(s) for 1A8M Structure Factors (141 Kb) Retrieve 1A8M in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1A8M from S2C, [Save to disk] Re-refined 1a8m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1A8M 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 1A8M

VIPERdb: visual, structural and computational analysis of 1A8M 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 1A8M, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1a8ma_, region A [Jmol] [rasmolscript] [script source]     - Domain d1a8mb_, region B [Jmol] [rasmolscript] [script source]     - Domain d1a8mc_, region C [Jmol] [rasmolscript] [script source] Fold representative 1a8m 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: [1a8m_A] [1a8m_B] [1a8m_C] SWISS-PROT database: [P01375] Domain organization of [TNFA_HUMAN] by SWISSPFAM Domain found in 1A8M: [TNF ] by SMART Alignments of the sequence of 1A8M with the sequences similar proteins can be viewed for 1A8M'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 1A8M

Community annotation for 1A8M at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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