6D1T | pdb_00006d1t

Complex of MBD1-MBD and methylated DNA

PDB DOI: https://doi.org/10.2210/pdb6D1T/pdb
NAKB: 6D1T

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-04-12 Released: 2018-05-09
Deposition Author(s): Liu, K., Xu, C., Tempel, W., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.269 (Depositor), 0.275 (DCC)
R-Value Work:
0.235 (Depositor), 0.241 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Complex of MBD1-MBD and methylated DNA

Liu, K., Xu, C., Tempel, W., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium

To be published.

Macromolecule Content

Total Structure Weight: 16.22 kDa
Atom Count: 1,038
Modeled Residue Count: 93
Deposited Residue Count: 103
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-CpG-binding domain protein 1	A	79	Homo sapiens	Mutation(s): 0 Gene Names: MBD1, CXXC3, PCM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIS9 (Homo sapiens) Explore Q9UIS9 Go to UniProtKB: Q9UIS9
PHAROS: Q9UIS9 GTEx: ENSG00000141644
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UIS9
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(GPCPCPAPAP(5CM)PGPTPTPGPGPC)-3')	B, C	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain L [auth C] SDF format, chain K [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth C], M [auth C], N [auth C], O [auth C]	UNKNOWN ATOM OR ION X		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.269 (Depositor), 0.275 (DCC)
R-Value Work: 0.235 (Depositor), 0.241 (DCC)
R-Value Observed: 0.238 (Depositor)

Diffraction Data:

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.574	α = 90
b = 74.193	β = 90
c = 138.872	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-05-09

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2018-05-09
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary