1KD1 Co-crystal Structure of Spiramycin bound to the 50S Ribosomal Subunit of Haloarcula marismortui date
authors Hansen, J.L., Ippolito, J.A., Ban, N., Nissen, P., Moore, P.B., Steitz, T.A.
compound source
symmetry
R_factor
R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.00
ligand CD, CL, K, MG, NA, SPR enzyme
related structures by homologous chain: 1K8A, 1K9M
Gene
Ontology
ChainFunctionProcessComponent
1


2


3


4


C


D


E


F


G


H
  • ribonuclease P activity


  • I


    J


    K


    L


    M


    N


    O


    P


    Q


    R


    S


    T


    U


    V


    W


    X


    Y


    Z


    Primary referenceThe structures of four macrolide antibiotics bound to the large ribosomal subunit., Hansen JL, Ippolito JA, Ban N, Nissen P, Moore PB, Steitz TA, Mol Cell 2002 Jul;10(1):117-28. PMID:12150912
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2000 Kb) [Save to disk]
  • Biological Unit Coordinates (1kd1.pdb1.gz) 1961 Kb
  • LPC: Ligand-Protein Contacts for 1KD1
  • CSU: Contacts of Structural Units for 1KD1
  • Likely Quarternary Molecular Structure file(s) for 1KD1
  • Structure Factors (5209 Kb)
  • Retrieve 1KD1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KD1 from S2C, [Save to disk]
  • Re-refined 1kd1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1KD1 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 1KD1
  • 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
  • 3D motif for 1KD1, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kd11_, region 1 [Jmol] [rasmolscript] [script source]
        - Domain d1kd12_, region 2 [Jmol] [rasmolscript] [script source]
        - Domain d1kd13_, region 3 [Jmol] [rasmolscript] [script source]
        - Domain d1kd14_, region 4 [Jmol] [rasmolscript] [script source]
        - Domain d1kd1c2, region C:1-90 [Jmol] [rasmolscript] [script source]
        - Domain d1kd1c1, region C:91-237 [Jmol] [rasmolscript] [script source]
        - Domain d1kd1d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1kd1e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1kd1f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1kd1g1, region G:1-79 [Jmol] [rasmolscript] [script source]
        - Domain d1kd1g2, region G:80-172 [Jmol] [rasmolscript] [script source]
        - Domain d1kd1h_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1kd1i_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1kd1j_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1kd1k_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1kd1l_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1kd1m_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1kd1n_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1kd1o_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1kd1p_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1kd1q_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1kd1r_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1kd1s_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1kd1t_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1kd1u_, region U [Jmol] [rasmolscript] [script source]
        - Domain d1kd1v_, region V [Jmol] [rasmolscript] [script source]
        - Domain d1kd1w_, region W [Jmol] [rasmolscript] [script source]
        - Domain d1kd1x_, region X [Jmol] [rasmolscript] [script source]
        - Domain d1kd1y_, region Y [Jmol] [rasmolscript] [script source]
        - Domain d1kd1z_, region Z [Jmol] [rasmolscript] [script source]
  • Fold representative 1kd1 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: [1kd1_I] [1kd1_U] [1kd1_Y] [1kd1_V] [1kd1_X] [1kd1_E] [1kd1_F] [1kd1_O] [1kd1_H] [1kd1_Z] [1kd1_Q] [1kd1_G] [1kd1_W] [1kd1_1] [1kd1_A] [1kd1_B] [1kd1] [1kd1_K] [1kd1_M] [1kd1_R] [1kd1_N] [1kd1_T] [1kd1_P] [1kd1_4] [1kd1_L] [1kd1_C] [1kd1_3] [1kd1_J] [1kd1_S] [1kd1_2] [1kd1_D]
  • SWISS-PROT database: [P60617] [P29198] [P22450] [P60618] [P12737] [P12733] [P14123] [P14119] [P12734] [P10970] [P12732] [P14116] [P10972] [P10971] [P20276] [P14121] [P18138] [P12736] [P60619] [P32410] [P22452] [P20279] [P32411] [P12735] [P14124] [P14135] [P12743] [P15825]
  • Domain organization of [RL10_HALMA] [RL13_HALMA] [RL14_HALMA] [RL15E_HALMA] [RL15_HALMA] [RL18E_HALMA] [RL18_HALMA] [RL19_HALMA] [RL21_HALMA] [RL22_HALMA] [RL23_HALMA] [RL24E_HALMA] [RL24_HALMA] [RL29_HALMA] [RL2_HALMA] [RL30_HALMA] [RL31_HALMA] [RL32_HALMA] [RL37A_HALMA] [RL37_HALMA] [RL39_HALMA] [RL3_HALMA] [RL44_HALMA] [RL4_HALMA] [RL5_HALMA] [RL6_HALMA] [RL7A_HALMA] [RLA0_HALMA] by SWISSPFAM
  • Domains found in 1KD1: [HhH1] [KOW] [Ribosomal_L14] [Ribosomal_L15e] [Ribosomal_L19e] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_L31e] [Ribosomal_L32e] [TRASH ] by SMART
  • Other resources with information on 1KD1
  • Community annotation for 1KD1 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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