9CKJ | pdb_00009ckj

Co-crystal structure of 53BP1 tandem Tudor domains in complex with UNC9512

PDB DOI: https://doi.org/10.2210/pdb9CKJ/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-09 Released: 2024-10-30
Deposition Author(s): Zeng, H., Dong, A., Shell, D.J., Foley, C., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.261 (Depositor), 0.282 (DCC)
R-Value Work:
0.219 (Depositor), 0.232 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Co-crystal structure of 53BP1 tandem Tudor domains in complex with UNC9512

Zeng, H., Dong, A., Shell, D.J., Foley, C., Arrowsmith, C.H., Edwards, A.M., Halabelian, L.

To be published.

Macromolecule Content

Total Structure Weight: 87.62 kDa
Atom Count: 5,979
Modeled Residue Count: 715
Deposited Residue Count: 744
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TP53-binding protein 1	A, B, C, D, E A, B, C, D, E, F	124	Homo sapiens	Mutation(s): 0 Gene Names: TP53BP1
UniProt & NIH Common Fund Data Resources
Find proteins for A6NNK5 (Homo sapiens) Explore A6NNK5 Go to UniProtKB: A6NNK5
GTEx: ENSG00000067369
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6NNK5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AY8 (Subject of Investigation/LOI) Query on A1AY8 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain K [auth E] SDF format, chain L [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain K [auth E] MOL2 format, chain L [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D] mmCIF format, chain K [auth E] mmCIF format, chain L [auth F]	G [auth A] H [auth B] I [auth C] J [auth D] K [auth E] G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	(3S)-1-[4-(4-methylpiperazin-1-yl)pyridine-2-carbonyl]-N-[(3M)-3-(3-oxo-2,3-dihydro-1H-isoindol-5-yl)phenyl]piperidine-3-carboxamide C₃₁ H₃₄ N₆ O₃ OYWGFOXQBJYTIR-DEOSSOPVSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain M [auth F] SDF format, chain N [auth F] MOL2 format, chain M [auth F] MOL2 format, chain N [auth F] mmCIF format, chain M [auth F] mmCIF format, chain N [auth F]	M [auth F], N [auth F]	UNKNOWN ATOM OR ION X		Interactions Focus chain M [auth F] Focus chain N [auth F] Interactions & Density Focus chain M [auth F] Focus chain N [auth F]