1M19

LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA

Structural Biology Knowledgebase: 1M19 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.214

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1M19

Classification: STRUCTURAL PROTEIN / DNA

Total Structure Weight: 200208.58


Macromolecule Entities
Molecule Chains Length Organism Details
Histone H3.2 A, E 135 Xenopus laevis Mutation: R486S
Gene Name(s): h3f3c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H4 B, F 102 Xenopus laevis Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H2A.1 C, G 129 Xenopus laevis Mutation: G899R
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H2B.1 D, H 125 Xenopus laevis Mutation: S1229T
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
Palindromic 146 Base Pair DNA Fragment I, J 146 synthetic

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

I, J 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID
C5 H7 N3 O2
PPQDQYBXCYQCNH-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PYB
Query on PYB

I, J 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID
C6 H8 N2 O2
MUEOQEUSJMFYHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ABU
Query on ABU

I, J GAMMA-AMINO-BUTANOIC ACID
GAMMA(AMINO)-BUTYRIC ACID (Synonym)
C4 H9 N O2
BTCSSZJGUNDROE-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DIB
Query on DIB

I, J 3-AMINO-(DIMETHYLPROPYLAMINE)
C5 H14 N2
IUNMPGNGSSIWFP-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BAL
Query on BAL

I, J BETA-ALANINE
C3 H7 N O2
UCMIRNVEIXFBKS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

E, I, J MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.214
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 107.04 α = 90.00
b = 109.66 β = 90.00
c = 183.02 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-06-18
  • Released Date: 2003-02-18
  • Deposition author(s): Suto, R.K., Edayathumangalam, R.S., White, C.L., Melander, C., Gottesfeld, J.M., Dervan, P.B., Luger, K.

Revision History

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