Macromolecule Content

Total Structure Weight: 31760.23
Atom Count: 2120
Residue Count: 194
Unique protein chains: 1
Unique nucleic acid chains: 1

6CC8

Crystal structure MBD3 MBD domain in complex with methylated CpG DNA

DOI: 10.2210/pdb6CC8/pdb

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli BL21

Deposited: 2018-02-06 Released: 2018-04-04
Deposition Author(s): Liu, K., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.259
R-Value Work: 0.224

wwPDB Validation3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure MBD3 MBD domain in complex with methylated CpG DNA

Liu, K., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J.

To be published.

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Methyl-CpG-binding domain protein 3	A, B	73	Homo sapiens	Mutation(s): 0 Gene Names: MBD3
Find proteins for O95983 (Homo sapiens) Go to Gene View: MBD3 Go to UniProtKB: O95983
Protein Feature View Full Protein Feature View for O95983

Entity ID: 2
Molecule	Chains	Length	Organism
methylated CpG DNA	C,D,E,F	12	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
UNX Query on UNX Download SDF File Download CCD File	A, B, C, E	UNKNOWN ATOM OR ION X *		Ligand Interaction
UNK Query on UNK Download SDF File Download CCD File	F	UNKNOWN C₄ H₉ N O₂ QWCKQJZIFLGMSD-VKHMYHEASA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
5CM Query on 5CM	C, D, E, F	DNA LINKING	C₁₀ H₁₆ N₃ O₇ P		DC

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.259
R-Value Work: 0.224
Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 71.550	α = 90.00
b = 36.640	β = 92.77
c = 130.930	γ = 90.00

Software Package:

Software Name	Purpose
Aimless	data scaling
MOLREP	phasing
PHASER	phasing
XDS	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

Deposited Date: 2018-02-06
Released Date: 2018-04-04
Deposition Author(s): Liu, K., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History

Version 1.0: 2018-04-04
Type: Initial release

The RCSB PDB is funded by a grant (DBI-1338415) from the National Science Foundation, the National Institutes of Health, and the US Department of Energy.