5MU8 Cytokine date Jan 12, 2017
title Human Tnf-Alpha In Complex With Jnj525
authors J.M.Blevitt, M.D.Hack, K.L.Herman, P.F.Jackson, P.J.Krawczuk, A.D A.X.Liu, T.Mirzadegan, M.I.Nelen, A.P.Patrick, S.Steinbacher, M. K.J.Lumb
compound source
Molecule: Tumor Necrosis Factor
Chain: A, B, C, D, F, G, H, I, J, K, L, M, N, O, P, Q, R, S W, X, Y, Z, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, T, U, V, W;
Fragment: Unp Residues 77-233
Synonym: Cachectin,Tnf-Alpha,Tumor Necrosis Factor Ligand S Member 2,Tnf-A;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnf, Tnfa, Tnfsf2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.211 R_Free 0.300
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.888 118.348 186.747 97.57 94.31 98.75
method X-Ray Diffractionresolution 3.00 Å
ligand JNI enzyme
Gene
Ontology
ChainFunctionProcessComponent
S, a, T, N, K, d, Y, j, Z, u, k, g, t, e, J, W, v, s, B, H, c, q, b, D, I, G, U, w, F, r, V, Q, h, M, C, L, f, i, A, n, O, X, P, m, l, p, R, o


Primary referenceStructural Basis of Small-Molecule Aggregate Induced Inhibition of a Protein-Protein Interaction., Blevitt JM, Hack MD, Herman KL, Jackson PF, Krawczuk PJ, Lebsack AD, Liu AX, Mirzadegan T, Nelen MI, Patrick AN, Steinbacher S, Milla ME, Lumb KJ, J Med Chem. 2017 Mar 16. PMID:28300404
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2442 Kb) [Save to disk]
  • Biological Unit Coordinates (5mu8.pdb1.gz) 113 Kb
  • Biological Unit Coordinates (5mu8.pdb2.gz) 117 Kb
  • Biological Unit Coordinates (5mu8.pdb3.gz) 114 Kb
  • Biological Unit Coordinates (5mu8.pdb4.gz) 115 Kb
  • Biological Unit Coordinates (5mu8.pdb5.gz) 114 Kb
  • Biological Unit Coordinates (5mu8.pdb6.gz) 115 Kb
  • Biological Unit Coordinates (5mu8.pdb7.gz) 113 Kb
  • Biological Unit Coordinates (5mu8.pdb8.gz) 117 Kb
  • Biological Unit Coordinates (5mu8.pdb9.gz) 113 Kb
  • LPC: Ligand-Protein Contacts for 5MU8
  • CSU: Contacts of Structural Units for 5MU8
  • Structure Factors (3852 Kb)
  • Retrieve 5MU8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5MU8 from S2C, [Save to disk]
  • Re-refined 5mu8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5MU8 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 5MU8
  • 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
  • Fold representative 5mu8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5mu8_b] [5mu8_Z] [5mu8_D] [5mu8_r] [5mu8_X] [5mu8_S] [5mu8_w] [5mu8_T] [5mu8_F] [5mu8_I] [5mu8_U] [5mu8_N] [5mu8_Y] [5mu8_o] [5mu8_c] [5mu8_p] [5mu8_A] [5mu8_W] [5mu8_Q] [5mu8_d] [5mu8_l] [5mu8_s] [5mu8_G] [5mu8_q] [5mu8_e] [5mu8_B] [5mu8_i] [5mu8_H] [5mu8_h] [5mu8_t] [5mu8_a] [5mu8_V] [5mu8_L] [5mu8_J] [5mu8_C] [5mu8_K] [5mu8_P] [5mu8] [5mu8_k] [5mu8_M] [5mu8_n] [5mu8_u] [5mu8_m] [5mu8_f] [5mu8_R] [5mu8_O] [5mu8_g] [5mu8_v] [5mu8_j]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5MU8
  • Community annotation for 5MU8 at PDBWiki (http://pdbwiki.org)

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