1Q7Y

Crystal Structure of CCdAP-Puromycin bound at the Peptidyl transferase center of the 50S ribosomal subunit

Structural Biology Knowledgebase: 1Q7Y SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.225

Literature

Macromolecules
Sequence Display for 1Q7Y

Classification: RIBOSOME

Total Structure Weight: 1459605.88


Macromolecule Entities
Molecule Chains Length Organism Details
50S ribosomal protein L2P C 239 Haloarcula marismortui Gene Name(s): rpl2 rrnAC1608
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3P D 337 Haloarcula marismortui Mutation: ΔP310, F310R
Gene Name(s): rpl3 rrnAC1611
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4E E 246 Haloarcula marismortui Gene Name(s): rpl4 rrnAC1610
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5P F 176 Haloarcula marismortui Gene Name(s): rpl5 rrnAC1598
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6P G 177 Haloarcula marismortui Gene Name(s): rpl6 rrnAC1596
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L7Ae H 119 Haloarcula marismortui Gene Name(s): rpl7ae rrnAC0103
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Acidic ribosomal protein P0 homolog I 348 Haloarcula marismortui Gene Name(s): rpl10 rpl10e rplP0 rrnAC1417
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
L10 Ribosomal Protein J 167 Haloarcula marismortui Gene Name(s): rpl10e rrnAC2357
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13P K 145 Haloarcula marismortui Gene Name(s): rpl13 rrnAC0065
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14P L 132 Haloarcula marismortui Gene Name(s): rpl14 rrnAC1602
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15P M 164 Haloarcula marismortui Gene Name(s): rpl15 rrnAC1590
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
L15 Ribosomal Protein N 194 Haloarcula marismortui Gene Name(s): rpl15e rrnAC2065
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18P O 186 Haloarcula marismortui Gene Name(s): rpl18 rrnAC1593
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18e P 115 Haloarcula marismortui Gene Name(s): rpl18e rrnAC0064
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19E Q 148 Haloarcula marismortui Mutation: Y71K
Gene Name(s): rpl19e rrnAC1594
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21e R 95 Haloarcula marismortui Gene Name(s): rpl21e rrnAC0260
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22P S 154 Haloarcula marismortui Gene Name(s): rpl22 rrnAC1606
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23P T 84 Haloarcula marismortui Gene Name(s): rpl23p rrnAC1609
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24P U 119 Haloarcula marismortui Gene Name(s): rpl24p rrnAC1601
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24E V 66 Haloarcula marismortui
50S ribosomal protein L29P W 70 Haloarcula marismortui Gene Name(s): rpl29p rrnAC1604
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L30P X 154 Haloarcula marismortui Gene Name(s): rpl30p rrnAC1591
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L31e Y 91 Haloarcula marismortui Gene Name(s): rpl31e rrnAC3113
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32E Z 240 Haloarcula marismortui Gene Name(s): rpl32e rrnAC1595
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
L37Ae 50S ribosomal protein 1 73 Haloarcula marismortui Gene Name(s): rpl37ae rrnAC1669
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L37e 2 56 Haloarcula marismortui Gene Name(s): rpl37e rrnAC0797.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L39e 3 48 Haloarcula marismortui Mutation: ΔR31
Gene Name(s): rpl39e rrnAC3112
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S 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 ribosomal rna A 2922 Haloarcula marismortui
5S ribosomal RNA B 122 Haloarcula marismortui
CCdA-P-Puromycin 5 3 synthetic peptidyl transferase intermediate analogue CONTAINS PUROMYCIN

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PUY
Query on PUY

5 PUROMYCIN
C22 H29 N7 O5
RXWNCPJZOCPEPQ-NVWDDTSBSA-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)
PO4
Query on PO4

5 PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
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, 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, 5, 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 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: 3.2 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.225
  • 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: 2003-08-20
  • Released Date: 2003-10-07
  • Deposition author(s): Hansen, J.L., Schmeing, T.M., Moore, P.B., Steitz, T.A.

Revision History

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