3SMT | pdb_00003smt

Crystal structure of human SET domain-containing protein3

PDB DOI: https://doi.org/10.2210/pdb3SMT/pdb

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

Deposited: 2011-06-28 Released: 2011-07-20
Deposition Author(s): Dong, A., Zeng, H., Walker, J.R., Loppnau, P., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Wu, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free:
0.259 (Depositor), 0.260 (DCC)
R-Value Work:
0.208 (Depositor), 0.212 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of human SET domain-containing protein3

Zeng, H., Dong, A., Walker, J.R., Loppnau, P., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Wu, H.

To be published.

Macromolecule Content

Total Structure Weight: 58.33 kDa
Atom Count: 4,067
Modeled Residue Count: 465
Deposited Residue Count: 497
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 setd3	A	497	Homo sapiens	Mutation(s): 0 Gene Names: SETD3, C14orf154 EC: 2.1.1.43 (PDB Primary Data), 2.1.1.85 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q86TU7 (Homo sapiens) Explore Q86TU7 Go to UniProtKB: Q86TU7
PHAROS: Q86TU7 GTEx: ENSG00000183576
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86TU7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM 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]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ARS Query on ARS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	ARSENIC As RBFQJDQYXXHULB-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
UNX Query on UNX Download:Ideal Coordinates CCD File 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 R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain J [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 R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain J [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 R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain J [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] L [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]	UNKNOWN ATOM OR ION X		Interactions 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] Interactions & Density 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]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.259 (Depositor), 0.260 (DCC)
R-Value Work: 0.208 (Depositor), 0.212 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.864	α = 90
b = 113.864	β = 90
c = 83.57	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
BUSTER	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-07-20

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2011-07-20
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary