NMR Ensemble

1BYJ

GENTAMICIN C1A A-SITE COMPLEX

Structural Biology Knowledgebase: 1BYJ SBKB.org


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 38
  • Conformers Submitted: 38
  • Selection Criteria: Least Restraint Violation

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1BYJ

Classification: RNA

Total Structure Weight: 9109.82

Macromolecule Entities
Molecule Chains Length Organism Details
RNA (16S RNA) A 27 synthetic 16S RIBOSOMAL RNA (NTS 1404-1412/1488-1497) COMPLEXED WITH GENTAMICIN C1A

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GE3
Query on GE3

A 5-METHYL-4-METHYLAMINO-TETRAHYDRO-PYRAN-2,3,5- TRIOL
C7 H15 N O4
VXWORWYFOFDZLY-JWXFUTCRSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GE1
Query on GE1

A 3,4-DIDEOXY-2,6-AMINO-ALPHA-D GALACTOPYRANOSE
C6 H14 N2 O2
FGFITZOBEYBNGG-JKUQZMGJSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GE2
Query on GE2

A 3,5-DIAMINO-CYCLOHEXANOL
C6 H14 N2 O
ORKQZIAHTZABIG-FPFOFBBKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
GE1 N/A in BindingDB
N/A in BindingMoad
Kd: 2000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 38
  • Conformers Submitted: 38
  • Selection Criteria: LEAST RESTRAINT VIOLATION

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 1998-10-16
  • Released Date: 1999-10-29
  • Deposition author(s): Yoshizawa, S., Fourmy, D., Puglisi, J.D.

Revision History

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