486D

X-RAY CRYSTAL STRUCTURES OF 70S RIBOSOME FUNCTIONAL COMPLEXES

Structural Biology Knowledgebase: 486D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.5 Å
  • R-Value Work:

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 486D

Classification: RIBOSOME

Total Structure Weight: 111500.91

Macromolecule Entities
Molecule Chains Length Organism Details
P-SITE TRNA OF 70S RIBOSOME A 74 Escherichia coli
P-SITE CODON OF 70S RIBOSOME B 3 synthetic
A-SITE TRNA OF 70S RIBOSOME C 72 Saccharomyces cerevisiae
A-SITE CODON OF 70S RIBOSOME D 3 synthetic
E-SITE TRNA OF 70S RIBOSOME E 72 Thermus thermophilus
PENULTIMATE STEM OF 16S RRNA IN THE 70S RIBOSOME F 85 Thermus thermophilus
900 STEM-LOOP OF 16S RRNA IN THE 70S RIBOSOME G 33 Thermus thermophilus

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
IR
Query on IR

F IRIDIUM ION
Ir
MOHYGSBMXIJZBJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 11 Unique
ID Chains Type Formula 2D Diagram Parent
PSU
Query on PSU
A, C, E RNA LINKING C9 H13 N2 O9 P U
H2U
Query on H2U
A, C, E RNA LINKING C9 H15 N2 O9 P U
M2G
Query on M2G
A, C RNA LINKING C12 H18 N5 O8 P G
OMC
Query on OMC
A RNA LINKING C10 H16 N3 O8 P C
YYG
Query on YYG
A RNA LINKING C21 H29 N6 O12 P G
5MC
Query on 5MC
A, C, E RNA LINKING C10 H16 N3 O8 P C
5MU
Query on 5MU
A, C, E RNA LINKING C10 H15 N2 O9 P U
2MG
Query on 2MG
C RNA LINKING C11 H16 N5 O8 P G
1MG
Query on 1MG
C, E RNA LINKING C11 H16 N5 O8 P G
7MG
Query on 7MG
C RNA LINKING C11 H18 N5 O8 P G
1MA
Query on 1MA
C RNA LINKING C11 H16 N5 O7 P A

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.5 Å
  • R-Value Observed:
  • Space Group: I 4 2 2

Unit Cell:

Length (Å) Angle (°)
a = 508.02 α = 90.00
b = 508.02 β = 90.00
c = 802.79 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 1999-09-09
  • Released Date: 1999-10-04
  • Deposition author(s): Cate, J.H., Yusupov, M.M., Yusupova, G.Zh., Earnest, T.N., Noller, H.F.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update