2C7P

HhaI DNA methyltransferase complex with oligonucleotide containing 2- aminopurine opposite to the target base (GCGC:GMPC) and SAH

Structural Biology Knowledgebase: 2C7P SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.196

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2C7P

Classification: TRANSFERASE / DNA

Total Structure Weight: 45662.49


Macromolecule Entities
Molecule Chains Length Organism Details
MODIFICATION METHYLASE HHAI A 327 Haemophilus haemolyticus EC#: 2.1.1.37 IUBMB
Gene Name(s): hhaIM
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*G*GP*AP*TP*GP*(5CM*2PR)*CP*TP*GP*AP*C)-3' C 12 Synthetic construct
5'-D(*G*TP*CP*AP*GP*CP*GP*CP*AP*TP*CP*C)-3' D 12 Synthetic construct

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SAH
Query on SAH

A S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EPE
Query on EPE

A 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CIT
Query on CIT

A CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
5CM
Query on 5CM
C DNA LINKING C10 H16 N3 O7 P DC
2PR
Query on 2PR
C DNA LINKING C10 H14 N5 O6 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.196
  • Space Group: H 3 2

Unit Cell:

Length (Å) Angle (°)
a = 94.85 α = 90.00
b = 94.85 β = 90.00
c = 313.03 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-11-25
  • Released Date: 2005-12-14
  • Deposition author(s): Neely, R.K., Daujotyte, D., Grazulis, S., Magennis, S.W., Dryden, D.T.F., Klimasauskas, S., Jones, A.C.

Revision History

  • 2014-01-29
    Type: Non-polymer description | Details: HETSYN,FORMUL,HETNAM,HET
  • 2014-01-29
    Type: Geometry validation | Details: REMARK 500
  • 2014-01-29
    Type: Version format compliance | Details: REMARK 4
  • 2014-01-29
    Type: Polymer description | Details: COMPND,SEQRES
  • 2014-01-29
    Type: Refinement description | Details: REMARK 3
  • 2014-01-29
    Type: Other | Details: REMARK 375,MODRES,HEADER,REMARK 525
  • 2014-01-29
    Type: Atom nomenclature | Details: HETATM
  • 2014-01-29
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2014-01-29
    Type: Linkage | Details: LINK
  • 2014-01-29
    Type: Function and keywords | Details: KEYWDS
  • 2014-01-29
    Type: Source and taxonomy | Details: SOURCE
  • 2014-01-29
    Type: Entry title | Details: TITLE