7SS1 | pdb_00007ss1

The structure of NTMT1 in complex with compound GD433

PDB DOI: https://doi.org/10.2210/pdb7SS1/pdb

Classification: TRANSFERASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-11-09 Released: 2022-11-16
Deposition Author(s): Yadav, R., Guangping, D., Deng, Y., Huang, R., Noinaj, N.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.299 (Depositor), 0.293 (DCC)
R-Value Work:
0.248 (Depositor), 0.243 (DCC)
R-Value Observed:
0.252 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7SS1

Ligand Structure Quality Assessment

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

Literature

Discovery of a first-in-class small molecule inhibitor for Protein N-terminal methyltransferases 1/2

Yadav, R., Guangping, D., Deng, Y., Huang, R., Noinaj, N.

To be published.

Macromolecule Content

Total Structure Weight: 56.22 kDa
Atom Count: 3,625
Modeled Residue Count: 441
Deposited Residue Count: 482
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal Xaa-Pro-Lys N-methyltransferase 1	A, B	241	Homo sapiens	Mutation(s): 0 Gene Names: NTMT1, C9orf32, METTL11A, NRMT, NRMT1, AD-003 EC: 2.1.1.244
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BV86 (Homo sapiens) Explore Q9BV86 Go to UniProtKB: Q9BV86
PHAROS: Q9BV86 GTEx: ENSG00000148335
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BV86
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AKF (Subject of Investigation/LOI) Query on AKF Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	(1R,3S,4R)-1-azabicyclo[2.2.2]octan-3-yl {2-[2-(4-fluoro-3-hydroxyphenyl)-1,3-thiazol-4-yl]propan-2-yl}carbamate C₂₀ H₂₄ F N₃ O₃ S LRJXHGILPIXDQG-MRXNPFEDSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.299 (Depositor), 0.293 (DCC)
R-Value Work: 0.248 (Depositor), 0.243 (DCC)
R-Value Observed: 0.252 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.909	α = 90
b = 89.909	β = 90
c = 141.542	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-11-16
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2024-10-30
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.