8CGD Ribosome date Feb 03, 2023
title Clindamycin Bound To The 50s Subunit
authors H.Paternoga, T.O.Koller, B.Beckert, D.N.Wilson
compound source
Molecule: Large Ribosomal Subunit Protein Bl33
Chain
Synonym: 50s Ribosomal Protein L33
 Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Bl34
Chain: 1
Synonym: 50s Ribosomal Protein L34
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Bl35
Chain: 2
Synonym: 50s Ribosomal Protein L35,Ribosomal Protein A
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Bl36a
Chain: 3
Synonym: 50s Ribosomal Protein L36,Ribosomal Protein B
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: 23s Rrna
Chain: a
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: 5s Rrna
Chain: b
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Ul2
Chain: c
Synonym: 50s Ribosomal Protein L2
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Ul3
Chain: d
Synonym: 50s Ribosomal Protein L3
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Ul4
Chain: e
Synonym: 50s Ribosomal Protein L4
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Ul5
Chain: f
Synonym: 50s Ribosomal Protein L5
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Ul6
Chain: g
Synonym: 50s Ribosomal Protein L6
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Bl9
Chain: h
Synonym: 50s Ribosomal Protein L9
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Ul13
Chain: I
Synonym: 50s Ribosomal Protein L13
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Ul14
Chain: j
Synonym: 50s Ribosomal Protein L14
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: 50s Ribosomal Protein L15
Chain: k
Synonym: Large Ribosomal Subunit Protein Ul15
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Ul16
Chain: l
Synonym: 50s Ribosomal Protein L16
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Bl17
Chain: m
Synonym: 50s Ribosomal Protein L17
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Ul18
Chain: n
Synonym: 50s Ribosomal Protein L18
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Bl19
Chain: o
Synonym: 50s Ribosomal Protein L19
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Bl20
Chain: p
Synonym: 50s Ribosomal Protein L20
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Bl21
Chain: q
Synonym: 50s Ribosomal Protein L21
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Ul22
Chain: r
Synonym: 50s Ribosomal Protein L22
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Ul23
Chain: s
Synonym: 50s Ribosomal Protein L23
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Ul24
Chain: t
Synonym: 50s Ribosomal Protein L24
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: 50s Ribosomal Protein L25
Chain: u
Synonym: Large Ribosomal Subunit Protein Bl25
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Bl27
Chain: v
Synonym: 50s Ribosomal Protein L27
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Bl28
Chain: w
Synonym: 50s Ribosomal Protein L28
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Ul29
Chain: x
Synonym: 50s Ribosomal Protein L29
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Ul30
Chain: y
Synonym: 50s Ribosomal Protein L30
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895

Molecule: Large Ribosomal Subunit Protein Bl32
Chain: z
Synonym: 50s Ribosomal Protein L32
Organism_scientific: Escherichia Coli Bw25113
Organism_taxid: 679895
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 1.98 Å
ligand 1MG, 2MA, 2MG, 3TD, 4D4, 5MC, 5MU, 6MZ, ACT, AM2, CLY, G7M, H2U, K, MEQ, MG, MS6, OMC, OMG, OMU, PSU, ZN enzyme
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1905 Kb) [Save to disk]
  • Biological Unit Coordinates (8cgd.pdb1.gz) 1849 Kb
  • LPC: Ligand-Protein Contacts for 8CGD
  • CSU: Contacts of Structural Units for 8CGD
  • Retrieve 8CGD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 8CGD from S2C, [Save to disk]
    • View 8CGD 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 8CGD
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [8cgd_0] [8cgd_w] [8cgd_j] [8cgd_v] [8cgd_g] [8cgd_1] [8cgd_d] [8cgd_p] [8cgd_z] [8cgd_y] [8cgd_o] [8cgd_e] [8cgd_s] [8cgd_m] [8cgd_n] [8cgd_k] [8cgd_a] [8cgd_t] [8cgd_i] [8cgd_h] [8cgd_f] [8cgd_u] [8cgd_x] [8cgd_q] [8cgd_c] [8cgd_l] [8cgd_2] [8cgd_3] [8cgd_b] [8cgd_r]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 8CGD
  • Community annotation for 8CGD at PDBWiki (http://pdbwiki.org)

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