3MT6 Hydrolase Antibiotic date Apr 30, 2010
title Structure Of Clpp From Escherichia Coli In Complex With Adep
authors Y.S.Chung
compound source
Molecule: Atp-Dependent Clp Protease Proteolytic Subunit
Chain: R, S, T, U, O, P, Q, Y, Z, a, b, V, W, X, M, L, K, J F, E, D, C, B, A, G;
Synonym: Adep1, Endopeptidase Clp, Caseinolytic Protease, P Ti, Heat Shock Protein F21.5;
Ec: 3.4.21.92
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12
Gene: B0437, Clpp, Jw0427, Lopp
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet9a

Molecule: Acyldepsipeptide 1
Chain: 1, 2, c, d, e, f, g, h, I, j, k, l, m, n, o, p, q, r W, X, Y, Z, 3, 4, U

Organism_scientific: Streptomyces Hawaiiensis
Organism_taxid: 67305
symmetry Space Group: P 1 21 1
R_factor 0.178 R_Free 0.204
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.254 121.150 276.170 90.00 91.38 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand MAA, MP8, MPD, OTT enzyme Hydrolase E.C.3.4.21.92 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
S, F, a, T, N, K, Y, E, V, Z, Q, M, C, L, A, J, O, W, X, P, B, H, b, D, R, I, G, U


Primary referenceAcyldepsipeptide antibiotics induce the formation of a structured axial channel in ClpP: A model for the ClpX/ClpA-bound state of ClpP., Li DH, Chung YS, Gloyd M, Joseph E, Ghirlando R, Wright GD, Cheng YQ, Maurizi MR, Guarne A, Ortega J, Chem Biol. 2010 Sep 24;17(9):959-69. PMID:20851345
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (931 Kb) [Save to disk]
  • Biological Unit Coordinates (3mt6.pdb1.gz) 459 Kb
  • Biological Unit Coordinates (3mt6.pdb2.gz) 469 Kb
  • LPC: Ligand-Protein Contacts for 3MT6
  • CSU: Contacts of Structural Units for 3MT6
  • Structure Factors (3730 Kb)
  • Retrieve 3MT6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3MT6 from S2C, [Save to disk]
  • Re-refined 3mt6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3MT6 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 3MT6
  • 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 3MT6, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3mt6_t] [3mt6_M] [3mt6_a] [3mt6_D] [3mt6_w] [3mt6_f] [3mt6_F] [3mt6_K] [3mt6_v] [3mt6_I] [3mt6_y] [3mt6_1] [3mt6] [3mt6_H] [3mt6_4] [3mt6_C] [3mt6_O] [3mt6_3] [3mt6_r] [3mt6_E] [3mt6_s] [3mt6_j] [3mt6_q] [3mt6_R] [3mt6_c] [3mt6_Y] [3mt6_i] [3mt6_L] [3mt6_A] [3mt6_k] [3mt6_J] [3mt6_Q] [3mt6_S] [3mt6_W] [3mt6_h] [3mt6_Z] [3mt6_X] [3mt6_n] [3mt6_z] [3mt6_T] [3mt6_g] [3mt6_d] [3mt6_P] [3mt6_V] [3mt6_G] [3mt6_u] [3mt6_N] [3mt6_o] [3mt6_x] [3mt6_2] [3mt6_b] [3mt6_U] [3mt6_B] [3mt6_m] [3mt6_e] [3mt6_p] [3mt6_l]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3MT6
  • Community annotation for 3MT6 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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