5JUW | pdb_00005juw

complex of Dot1l with SS148

PDB DOI: https://doi.org/10.2210/pdb5JUW/pdb

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

Deposited: 2016-05-10 Released: 2016-06-22
Deposition Author(s): Yu, W., Tempel, W., Li, Y., Spurr, S.S., Bayle, E.D., Fish, P.V., Schapira, M., 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: 2.28 Å
R-Value Free:
0.215 (Depositor), 0.228 (DCC)
R-Value Work:
0.189 (Depositor), 0.203 (DCC)
R-Value Observed:
0.190 (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

Complex of Dot1l with SS148

Yu, W., Tempel, W., Li, Y., Spurr, S.S., Bayle, E.D., Fish, P.V., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Brown, P.J.

To be published.

Macromolecule Content

Total Structure Weight: 48.39 kDa
Atom Count: 2,711
Modeled Residue Count: 324
Deposited Residue Count: 421
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase, H3 lysine-79 specific	A	421	Homo sapiens	Mutation(s): 0 Gene Names: DOT1L, KIAA1814, KMT4 EC: 2.1.1.43 (PDB Primary Data), 2.1.1.360 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TEK3 (Homo sapiens) Explore Q8TEK3 Go to UniProtKB: Q8TEK3
PHAROS: Q8TEK3 GTEx: ENSG00000104885
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TEK3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6NR Query on 6NR Download:Ideal Coordinates CCD File SDF format, chain X [auth A] MOL2 format, chain X [auth A] mmCIF format, chain X [auth A]	X [auth A]	(2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(4-azanyl-5-cyano-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]butanoic acid C₁₆ H₂₀ N₆ O₅ S XLTWYAYAFLGUEQ-OPYVMVOTSA-N		Interactions Focus chain X [auth A] Interactions & Density Focus chain X [auth A]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain J [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain J [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain J [auth A] mmCIF format, chain E [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [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], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain B [auth A] 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] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain B [auth A] 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] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
6NR	BindingDB: 5JUW	IC50: min: 13, max: 26 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.215 (Depositor), 0.228 (DCC)
R-Value Work: 0.189 (Depositor), 0.203 (DCC)
R-Value Observed: 0.190 (Depositor)

Diffraction Data:

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.258	α = 90
b = 153.258	β = 90
c = 50.723	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-06-22

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2016-06-22
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description