6C2F

MBD2 in complex with methylated DNA

PDB DOI: https://doi.org/10.2210/pdb6C2F/pdb
NAKB: 6C2F

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

Deposited: 2018-01-08 Released: 2018-02-14
Deposition Author(s): Liu, K., Xu, C., Tempel, W., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium, Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.242
R-Value Work: 0.211
R-Value Observed: 0.213

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

MBD2 in complex with 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: 96.79 kDa
Atom Count: 5,915
Modelled Residue Count: 552
Deposited Residue Count: 618
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-CpG-binding domain protein 2	A, D, G, J, M A, D, G, J, M, P	79	Homo sapiens	Mutation(s): 0 Gene Names: MBD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBB5 (Homo sapiens) Explore Q9UBB5 Go to UniProtKB: Q9UBB5
PHAROS: Q9UBB5 GTEx: ENSG00000134046
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UBB5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
12-mer DNA	B, E, H, K, N B, E, H, K, N, Q	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
12-mer DNA	C, F, I, L, O C, F, I, L, O, R	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 AA [auth M] SDF format, chain BA [auth M] SDF format, chain CA [auth P] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth G] SDF format, chain X [auth G] SDF format, chain Y [auth J] SDF format, chain Z [auth J] MOL2 format, chain AA [auth M] MOL2 format, chain BA [auth M] MOL2 format, chain CA [auth P] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth G] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth J] MOL2 format, chain Z [auth J] mmCIF format, chain AA [auth M] mmCIF format, chain BA [auth M] mmCIF format, chain CA [auth P] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain W [auth G] mmCIF format, chain X [auth G] mmCIF format, chain Y [auth J] mmCIF format, chain Z [auth J]	AA [auth M] BA [auth M] CA [auth P] S [auth A] T [auth A] AA [auth M], BA [auth M], CA [auth P], S [auth A], T [auth A], U [auth D], V [auth D], W [auth G], X [auth G], Y [auth J], Z [auth J]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth M] Focus chain BA [auth M] Focus chain CA [auth P] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth G] Focus chain X [auth G] Focus chain Y [auth J] Focus chain Z [auth J]