3BO5 | pdb_00003bo5

Crystal structure of methyltransferase domain of human Histone-lysine N-methyltransferase SETMAR

PDB DOI: https://doi.org/10.2210/pdb3BO5/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-12-17 Released: 2008-01-22
Deposition Author(s): Lunin, V.V., Wu, H., Ren, H., Dobrovetsky, E., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Plotnikov, A.N., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.199 (Depositor), 0.200 (DCC)
R-Value Work:
0.155 (Depositor), 0.150 (DCC)
R-Value Observed:
0.157 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The Crystal Structure of Methyltransferase Domain of Human Histone-lysine N-methyltransferase SETMAR in Complex With AdoHcy.

Wu, H., Lunin, V.V., Ren, H., Dobrovetsky, E., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Plotnikov, A.N.

To be published.

Macromolecule Content

Total Structure Weight: 33.13 kDa
Atom Count: 2,467
Modelled Residue Count: 269
Deposited Residue Count: 290
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SETMAR	A	290	Homo sapiens	Mutation(s): 2 Gene Names: SETMAR EC: 2.1.1.43 (PDB Primary Data), 3.1 (UniProt), 2.1.1.357 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q53H47 (Homo sapiens) Explore Q53H47 Go to UniProtKB: Q53H47
PHAROS: Q53H47 GTEx: ENSG00000170364
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q53H47
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
ZN Query on ZN 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 E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [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 E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.199 (Depositor), 0.200 (DCC)
R-Value Work: 0.155 (Depositor), 0.150 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.396	α = 90
b = 67.827	β = 105.93
c = 44.637	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-01-22

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-01-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2024-02-21
Changes: Data collection

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Crystal structure of methyltransferase domain of human Histone-lysine N-methyltransferase SETMAR

The Crystal Structure of Methyltransferase Domain of Human Histone-lysine N-methyltransferase SETMAR in Complex With AdoHcy.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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