1KC8

Co-crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit

Structural Biology Knowledgebase: 1KC8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.195

Literature

Macromolecules
Sequence Display for 1KC8

Classification: RIBOSOME

Total Structure Weight: 1459044.75


Macromolecule Entities
Molecule Chains Length Organism Details
RIBOSOMAL PROTEIN L2 C 239 Haloarcula marismortui Gene Name(s): rpl2 rrnAC1608
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L3 D 337 Haloarcula marismortui Mutation: ΔP310, F310R
Gene Name(s): rpl3 rrnAC1611
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L4 E 246 Haloarcula marismortui Gene Name(s): rpl4 rrnAC1610
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L5 F 176 Haloarcula marismortui Gene Name(s): rpl5 rrnAC1598
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L6 G 177 Haloarcula marismortui Gene Name(s): rpl6 rrnAC1596
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L7AE H 119 Haloarcula marismortui Gene Name(s): rpl7ae rrnAC0103
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L10 I 348 Haloarcula marismortui Gene Name(s): rpl10 rpl10e rplP0 rrnAC1417
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L10E J 167 Haloarcula marismortui Gene Name(s): rpl10e rrnAC2357
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L13 K 145 Haloarcula marismortui Gene Name(s): rpl13 rrnAC0065
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L14 L 132 Haloarcula marismortui Gene Name(s): rpl14 rrnAC1602
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L15 M 164 Haloarcula marismortui Gene Name(s): rpl15 rrnAC1590
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L15E N 194 Haloarcula marismortui Gene Name(s): rpl15e rrnAC2065
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L18 O 186 Haloarcula marismortui Gene Name(s): rpl18 rrnAC1593
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L18E P 115 Haloarcula marismortui Gene Name(s): rpl18e rrnAC0064
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L19E Q 148 Haloarcula marismortui Mutation: Y71K
Gene Name(s): rpl19e rrnAC1594
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L21E R 95 Haloarcula marismortui Gene Name(s): rpl21e rrnAC0260
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L22 S 154 Haloarcula marismortui Gene Name(s): rpl22 rrnAC1606
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L23 T 84 Haloarcula marismortui Gene Name(s): rpl23p rrnAC1609
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L24 U 119 Haloarcula marismortui Gene Name(s): rpl24p rrnAC1601
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L24E V 66 Haloarcula marismortui Gene Name(s): rpl24e rrnAC0104
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L29 W 70 Haloarcula marismortui Gene Name(s): rpl29p rrnAC1604
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L30 X 154 Haloarcula marismortui Gene Name(s): rpl30p rrnAC1591
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L31E Y 91 Haloarcula marismortui Gene Name(s): rpl31e rrnAC3113
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L32E Z 240 Haloarcula marismortui Gene Name(s): rpl32e rrnAC1595
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L37Ae 1 73 Haloarcula marismortui Gene Name(s): rpl37ae rrnAC1669
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L37E 2 56 Haloarcula marismortui Gene Name(s): rpl37e rrnAC0797.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L39E 3 48 Haloarcula marismortui Mutation: ΔR31
Gene Name(s): rpl39e rrnAC3112
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIBOSOMAL PROTEIN L44E 4 92 Haloarcula marismortui Gene Name(s): rpl44e rrnAC3514
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
23S RRNA A 2922 Haloarcula marismortui
5S RRNA B 122 Haloarcula marismortui

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BLS
Query on BLS

A BLASTICIDIN S
C17 H26 N8 O5
CXNPLSGKWMLZPZ-ZNIXKSQXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

1, 2, 4, P, V CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

4, A, C, D, K, M, N, O, P, S, Z CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

1, 4, A, B, C, L, U, Z MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B, C, E, J, K, M, N, R, S, T, U SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.195
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 212.90 α = 90.00
b = 300.47 β = 90.00
c = 575.18 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-11-07
  • Released Date: 2003-07-22
  • Deposition author(s): Hansen, J.L., Ban, N., Nissen, P., Moore, P.B., Steitz, T.A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4