1M18

LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA

Structural Biology Knowledgebase: 1M18 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.222

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1M18

Classification: STRUCTURAL PROTEIN / DNA

Total Structure Weight: 201947.58


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

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

I, J N-[5-[[4-[[5-[[5-[[5-[[5-[[3-[3-(dimethylamino)propylamino]- 3-oxidanylidene-propyl]carbamoyl]-1-methyl- pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3- yl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]- 1-methyl-pyrrol-3-yl]amino]-4-oxidanylidene- butyl]carbamoyl]-1-methyl-pyrrol-3-yl]-1- methyl-4-[[1-methyl-4-[(1-methylimidazol- 2-yl)carbonylamino]pyrrol-2-yl]carbonylamino]imidazole- 2-carboxamide
PYRROLE-IMIDAZOLE POLYAMIDE (Synonym)
C58 H71 N21 O10
TUWUDTOJENRSJG-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
MN
Query on MN

D, I, J MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.222
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 106.84 α = 90.00
b = 109.63 β = 90.00
c = 183.17 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

  • 2013-07-17
    Type: Non-polymer description | Details: Convert polyamide to a single ligand with subcomponents
  • 2013-07-17
    Type: Sequence database correspondence | Details: Create a sequence reference for the DNA
  • 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