3I55 Ribosome Antibiotic date Jul 03, 2009
title Co-Crystal Structure Of Mycalamide A Bound To The Large Ribo Subunit
authors G.Gurel, G.Blaha, T.A.Steitz, P.B.Moore
compound source
Molecule: 23s Ribosomal Rna
Chain
Organism_scientific: Haloarcula Marismortui Atcc 43049
Organism_taxid: 272569

Molecule: 50s Ribosomal Protein L2p
Chain: A
Synonym: Hmal2, Hl4

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L3p
Chain: B
Synonym: Hmal3, Hl1

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L4p
Chain: C
Synonym: Hmal4, Hl6

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L5p
Chain: D
Synonym: Hmal5, Hl13

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L6p
Chain: E
Synonym: Hmal6, Hl10

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L7ae
Chain: F
Synonym: Hs6

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L10e
Chain: G
Synonym: Ribosomal Protein L10, Acidic Ribosomal Protein P0 L10e, Hmal10;

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L10e
Chain: H

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L11p
Chain: I
Synonym: Hmal11

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L13p
Chain: J
Synonym: Hmal13

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L14p
Chain: K
Synonym: Hmal14, Hl27

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L15p
Chain: L
Synonym: Hmal15, Hl9

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L15e
Chain: M
Synonym: 50s Ribosomal Protein Lc12

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L18p
Chain: N
Synonym: Hmal18, Hl12

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L18e
Chain: O
Synonym: Hl29, L19

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L19e
Chain: P
Synonym: Hmal19, Hl24

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L21e
Chain: Q
Synonym: Hl31

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L22p
Chain: R
Synonym: Hmal22, Hl23

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L23p
Chain: S
Synonym: Hmal23, Hl25, L21

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L24p
Chain: T
Synonym: Hmal24, Hl16, Hl15

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L24e
Chain: U
Synonym: Hl21hl22

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L29p
Chain: V
Synonym: Hmal29, Hl33

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L30p
Chain: W
Synonym: Hmal30, Hl20, Hl16

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L31e
Chain: X
Synonym: L34, Hl30

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L32e
Chain: Y
Synonym: Hl5

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L37ae
Chain: Z

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L37e
Chain: 1
Synonym: L35e

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L39e
Chain: 2
Synonym: Hl39e, Hl46e

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L44e
Chain: 3
Synonym: La, Hla

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 5s Ribosomal Rna
Chain: 9

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Dnarna (5'-R(Cpcp(5aa)P(2op)P(Po2)Papcpc
Chain: 4
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 2 2 21
R_factor 0.210 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
211.324 299.649 574.241 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.11 Å
ligand 1MA, 2OP, 5AA, CD, CL, K, MG, MYL, NA, OMG, OMU, PO2, PSU, SR, UR3 enzyme
Gene
Ontology
ChainFunctionProcessComponent
1


2


3


A


B


C


D


E


F
  • ribonuclease P activity


  • G


    H


    I


    J


    K


    L


    M


    N


    O


    P


    Q


    R


    S


    T


    U


    V


    W


    X


    Y


    Z


    Primary referenceStructures of triacetyloleandomycin and mycalamide A bind to the large ribosomal subunit of Haloarcula marismortui., Gurel G, Blaha G, Steitz TA, Moore PB, Antimicrob Agents Chemother. 2009 Dec;53(12):5010-4. Epub 2009 Sep 8. PMID:19738021
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1979 Kb) [Save to disk]
  • Biological Unit Coordinates (3i55.pdb1.gz) 1947 Kb
  • LPC: Ligand-Protein Contacts for 3I55
  • CSU: Contacts of Structural Units for 3I55
  • Structure Factors (3072 Kb)
  • Retrieve 3I55 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3I55 from S2C, [Save to disk]
  • Re-refined 3i55 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3I55 in 3D
  • Proteopedia, because life has more than 2D.
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  • Visual 3D analysis of 3I55
  • 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 3I55, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3i55] [3i55_0] [3i55_V] [3i55_Y] [3i55_N] [3i55_I] [3i55_U] [3i55_2] [3i55_3] [3i55_9] [3i55_4] [3i55_F] [3i55_Z] [3i55_G] [3i55_W] [3i55_H] [3i55_B] [3i55_D] [3i55_L] [3i55_R] [3i55_E] [3i55_Q] [3i55_M] [3i55_K] [3i55_A] [3i55_O] [3i55_J] [3i55_P] [3i55_C] [3i55_T] [3i55_X] [3i55_S] [3i55_1]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3I55: [HhH1] [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L15e] [Ribosomal_L19e] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_L31e] [Ribosomal_L32e] [TRASH ] by SMART
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