3UWN | pdb_00003uwn

The 3-MBT repeat domain of L3MBTL1 in complex with a methyl-lysine mimic

PDB DOI: https://doi.org/10.2210/pdb3UWN/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-12-02 Released: 2012-03-07
Deposition Author(s): Zhong, N., Tempel, W., Wernimont, A.K., Graslund, S., Ingerman, L.A., Korboukh, V., Kireev, D.B., Gao, C., Frye, S.V., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Brown, P.J., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.267 (Depositor), 0.259 (DCC)
R-Value Work:
0.231 (Depositor), 0.233 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The 3-MBT repeat domain of L3MBTL1 in complex with a methyl-lysine mimic

Zhong, N., Tempel, W., Wernimont, A.K., Graslund, S., Ingerman, L.A., Korboukh, V., Kireev, D.B., Gao, C., Frye, S.V., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Brown, P.J., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 38.28 kDa
Atom Count: 2,710
Modeled Residue Count: 318
Deposited Residue Count: 331
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lethal(3)malignant brain tumor-like protein 1	A	331	Homo sapiens	Mutation(s): 0 Gene Names: L3MBTL1, KIAA0681, L3MBT, L3MBTL
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y468 (Homo sapiens) Explore Q9Y468 Go to UniProtKB: Q9Y468
PHAROS: Q9Y468 GTEx: ENSG00000185513
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y468
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UWN Query on UWN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	[2-(phenylamino)benzene-1,4-diyl]bis{[4-(pyrrolidin-1-yl)piperidin-1-yl]methanone} C₃₂ H₄₃ N₅ O₂ PQOOIERVZAXHBP-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain K [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain C [auth A] 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 A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain C [auth A] 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 A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
UWN	BindingDB: 3UWN	Kd: 9400 (nM) from 1 assay(s)
UWN	BindingDB: 3UWN	IC50: min: 2000, max: 8900 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.267 (Depositor), 0.259 (DCC)
R-Value Work: 0.231 (Depositor), 0.233 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.774	α = 90
b = 94.53	β = 90
c = 58.955	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-03-07

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2012-03-07
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description