6PDM | pdb_00006pdm

Crystal structure of Human Protein Arginine Methyltransferase 9 (PRMT9)

PDB DOI: https://doi.org/10.2210/pdb6PDM/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2019-06-19 Released: 2019-07-31
Deposition Author(s): Halabelian, L., Tempel, W., Zeng, H., Li, Y., Seitova, A., Hutchinson, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.260 (Depositor), 0.273 (DCC)
R-Value Work:
0.216 (Depositor), 0.230 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Human Protein Arginine Methyltransferase 9 (PRMT9)

Halabelian, L., Tempel, W., Zeng, H., Li, Y., Seitova, A., Hutchinson, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H.

To be published.

Macromolecule Content

Total Structure Weight: 80.49 kDa
Atom Count: 4,482
Modeled Residue Count: 614
Deposited Residue Count: 720
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 9	A	720	Homo sapiens	Mutation(s): 0 Gene Names: PRMT9, PRMT10 EC: 2.1.1.320
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P2P2 (Homo sapiens) Explore Q6P2P2 Go to UniProtKB: Q6P2P2
PHAROS: Q6P2P2 GTEx: ENSG00000164169
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6P2P2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] 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 E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] 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 E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] 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 E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [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]	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] 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.260 (Depositor), 0.273 (DCC)
R-Value Work: 0.216 (Depositor), 0.230 (DCC)
R-Value Observed: 0.219 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.812	α = 90
b = 83.802	β = 98.16
c = 65.711	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MR-Rosetta	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-07-31

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2019-07-31
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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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.