3MK3 Transferase date Apr 14, 2010
title Crystal Structure Of Lumazine Synthase From Salmonella Typhi
authors P.Kumar, M.Singh, S.Karthikeyan
compound source
Molecule: 6,7-Dimethyl-8-Ribityllumazine Synthase
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R V, W, X, Y, Z, 1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y;
Synonym: Dmrl Synthase, Lumazine Synthase, Riboflavin Synth Chain;
Ec: 2.5.1.78
Engineered: Yes
Organism_scientific: Salmonella Typhimurium
Organism_taxid: 99287
Strain: Lt2
Gene: Ribh, Stm0417
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-De3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28c
symmetry Space Group: P 1 21 1
R_factor 0.226 R_Free 0.264
crystal
cell
length a length b length c angle alpha angle beta angle gamma
154.234 151.503 235.032 90.00 97.08 90.00
method X-Ray Diffractionresolution 3.57 Å
ligand SO4 enzyme Transferase E.C.2.5.1.78 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
S, a, T, N, K, 7, d, Y, E, 2, j, y, Z, u, 1, k, g, t, e, J, W, v, s, B, H, c, q, b, D, I, G, U, w, F, r, x, V, Q, h, M, C, f, L, i, A, 6, n, O, 3, X, P, m, 9, l, 8, p, 4, R, o, 5


Primary referenceCrystal structure analysis of icosahedral lumazine synthase from Salmonella typhimurium, an antibacterial drug target., Kumar P, Singh M, Karthikeyan S, Acta Crystallogr D Biol Crystallogr. 2011 Feb;67(Pt 2):131-9. Epub 2011, Jan 15. PMID:21245535
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1324 Kb) [Save to disk]
  • Biological Unit Coordinates (3mk3.pdb1.gz) 1315 Kb
  • LPC: Ligand-Protein Contacts for 3MK3
  • CSU: Contacts of Structural Units for 3MK3
  • Structure Factors (917 Kb)
  • Retrieve 3MK3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3MK3 from S2C, [Save to disk]
  • Re-refined 3mk3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3MK3 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 3MK3
  • 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
  • 3D motif for 3MK3, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3mk3_U] [3mk3_h] [3mk3_M] [3mk3_y] [3mk3_V] [3mk3_d] [3mk3_E] [3mk3_m] [3mk3_1] [3mk3_Z] [3mk3_R] [3mk3_3] [3mk3_O] [3mk3_6] [3mk3_f] [3mk3_x] [3mk3_a] [3mk3_Q] [3mk3_A] [3mk3_N] [3mk3_B] [3mk3_G] [3mk3_p] [3mk3_t] [3mk3_P] [3mk3_F] [3mk3_2] [3mk3_e] [3mk3_S] [3mk3_J] [3mk3_8] [3mk3_7] [3mk3_q] [3mk3_i] [3mk3_v] [3mk3_4] [3mk3_I] [3mk3_D] [3mk3_9] [3mk3_Y] [3mk3_s] [3mk3_T] [3mk3_w] [3mk3_k] [3mk3_b] [3mk3_K] [3mk3_o] [3mk3_W] [3mk3_c] [3mk3_l] [3mk3_5] [3mk3_g] [3mk3] [3mk3_H] [3mk3_r] [3mk3_C] [3mk3_X] [3mk3_L] [3mk3_u] [3mk3_n] [3mk3_j]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3MK3
  • Community annotation for 3MK3 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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