8XPT | pdb_00008xpt

The Crystal Structure of EHMT1 from Biortus.

PDB DOI: https://doi.org/10.2210/pdb8XPT/pdb

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

Deposited: 2024-01-04 Released: 2024-01-24
Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Lin, D., Bao, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free:
0.262 (Depositor), 0.256 (DCC)
R-Value Work:
0.195 (Depositor), 0.200 (DCC)

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

The Crystal Structure of EHMT1 from Biortus.

Wang, F., Cheng, W., Yuan, Z., Lin, D., Bao, C.

To be published.

Macromolecule Content

Total Structure Weight: 134.29 kDa
Atom Count: 8,300
Modeled Residue Count: 1,009
Deposited Residue Count: 1,140
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 EHMT1	A, B, C, D	285	Homo sapiens	Mutation(s): 0 Gene Names: EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D EC: 2.1.1 (PDB Primary Data), 2.1.1.367 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9B1 (Homo sapiens) Explore Q9H9B1 Go to UniProtKB: Q9H9B1
PHAROS: Q9H9B1 GTEx: ENSG00000181090
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H9B1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain Q [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain W [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain W [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], Q [auth C], W [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain Q [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain Q [auth C] Focus chain W [auth D]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain BA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain BA [auth D] mmCIF format, chain V [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain BA [auth D]	BA [auth D], O [auth B], P [auth B], V [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain V [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain AA [auth D]	AA [auth D] F [auth A] G [auth A] H [auth A] I [auth A] AA [auth D], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], N [auth B], R [auth C], S [auth C], T [auth C], U [auth C], X [auth D], Y [auth D], Z [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]