1Q86

Crystal structure of CCA-Phe-cap-biotin bound simultaneously at half occupancy to both the A-site and P-site of the the 50S ribosomal Subunit.

Structural Biology Knowledgebase: 1Q86 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.234

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1Q86

Classification: RIBOSOME

Total Structure Weight: 1460273.17


Macromolecule Entities
Molecule Chains Length Organism Details
50S ribosomal protein L2P C 239 Haloarcula marismortui Gene Name(s): rpl2 rrnAC1608
50S ribosomal protein L3P D 337 Haloarcula marismortui Mutation: ΔP310, F310R
Gene Name(s): rpl3 rrnAC1611
50S ribosomal protein L4E E 246 Haloarcula marismortui Gene Name(s): rpl4 rrnAC1610
50S ribosomal protein L5P F 176 Haloarcula marismortui Gene Name(s): rpl5 rrnAC1598
50S ribosomal protein L6P G 177 Haloarcula marismortui Gene Name(s): rpl6 rrnAC1596
50S ribosomal protein L7Ae H 119 Haloarcula marismortui Gene Name(s): rpl7ae rrnAC0103
Acidic ribosomal protein P0 homolog I 348 Haloarcula marismortui Gene Name(s): rpl10 rpl10e rplP0 rrnAC1417
L10 Ribosomal Protein J 167 Haloarcula marismortui Gene Name(s): rpl10e rrnAC2357
50S ribosomal protein L13P K 145 Haloarcula marismortui Gene Name(s): rpl13 rrnAC0065
50S ribosomal protein L14P L 132 Haloarcula marismortui Gene Name(s): rpl14 rrnAC1602
50S ribosomal protein L15P M 164 Haloarcula marismortui Gene Name(s): rpl15 rrnAC1590
L15 Ribosomal Protein N 194 Haloarcula marismortui Gene Name(s): rpl15e rrnAC2065
50S ribosomal protein L18P O 186 Haloarcula marismortui Gene Name(s): rpl18 rrnAC1593
50S ribosomal protein L18e P 115 Haloarcula marismortui Gene Name(s): rpl18e rrnAC0064
50S ribosomal protein L19E Q 148 Haloarcula marismortui Mutation: Y71K
Gene Name(s): rpl19e rrnAC1594
50S ribosomal protein L21e R 95 Haloarcula marismortui Gene Name(s): rpl21e rrnAC0260
50S ribosomal protein L22P S 154 Haloarcula marismortui Gene Name(s): rpl22 rrnAC1606
50S ribosomal protein L23P T 84 Haloarcula marismortui Gene Name(s): rpl23p rrnAC1609
50S ribosomal protein L24P U 119 Haloarcula marismortui Gene Name(s): rpl24p rrnAC1601
50S ribosomal protein L24E V 66 Haloarcula marismortui Gene Name(s): rpl24e rrnAC0104
50S ribosomal protein L29P W 70 Haloarcula marismortui Gene Name(s): rpl29p rrnAC1604
50S ribosomal protein L30P X 154 Haloarcula marismortui Gene Name(s): rpl30p rrnAC1591
50S ribosomal protein L31e Y 91 Haloarcula marismortui Gene Name(s): rpl31e rrnAC3113
50S ribosomal protein L32E Z 240 Haloarcula marismortui Gene Name(s): rpl32e rrnAC1595
L37Ae 50S ribosomal protein 1 73 Haloarcula marismortui Gene Name(s): rpl37ae rrnAC1669
50S ribosomal protein L37e 2 56 Haloarcula marismortui Gene Name(s): rpl37e rrnAC0797.1
50S ribosomal protein L39e 3 48 Haloarcula marismortui Mutation: ΔR31
Gene Name(s): rpl39e rrnAC3112
50S ribosomal protein L44E 4 92 Haloarcula marismortui Gene Name(s): rpl44e rrnAC3514
Macromolecule Entities
Molecule Chains Length Organism Details
23S ribosomal rna A 2922 Haloarcula marismortui
5S ribosomal RNA B 122 Haloarcula marismortui
CCA-phenylalanine-cariotic-acid-biotin 5, 6 3 synthetic AN ANALOGUE OF PEPTIDYL-TRNA CONTAINS PHENYLALANINAL, cariotic-acid, AND BIOTIN

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

5, 6 PHENYLALANINAL
C9 H11 N O
CQIUZHAQYHXKRY-VIFPVBQESA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

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

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

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

1, 4, 6, A, B, C, D, L, U, Z MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.234
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 213.16 α = 90.00
b = 301.29 β = 90.00
c = 575.40 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

  • 2016-02-10
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4