407D

STRUCTURAL BASIS FOR RECOGNITION OF A-T AND T-A BASE PAIRS IN THE MINOR GROOVE OF B-DNA

  • Classification: DNA
  • Deposited: 1998-06-24 Released: 1998-10-19
  • Deposition author(s): Rees

Structural Biology Knowledgebase: 407D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.210

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 407D

Classification: DNA

Total Structure Weight: 7537.66

Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*CP*AP*GP*TP*AP*CP*TP*GP*G)-3') A, B 10 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HP1
Query on HP1

A, B IMIDAZOLE-PYRROLE-HYDROXYPYRROLE POLYAMIDE
IMIDAZOLE-HYDROXYPYRROLE-PYRROLE-PYRROLE- BETA ALANINE-DIMETHYLAMINO PROPYLAMIDE (Synonym)
C31 H40 N11 O6
HXEVGURSXJBSLI-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRS
Query on TRS

A 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
HP1 N/A in BindingDB
N/A in BindingMoad
Kd: 344 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.210
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 60.44 α = 90.00
b = 30.51 β = 120.47
c = 42.76 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 1998-06-24
  • Released Date: 1998-10-19
  • Deposition author(s): Rees

Revision History

  • 2011-11-16
    Type: Atom occupancy | Details: Atom occupancy
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4