Macromolecule Content

Total Structure Weight: 27.62 kDa
Atom Count: 1,446
Modelled Residue Count: 159
Deposited Residue Count: 237
Unique protein chains: 1

3RAY

Crystal structure of Methyltransferase domain of human PR domain-containing protein 11

PDB DOI: https://doi.org/10.2210/pdb3RAY/pdb

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

Deposited: 2011-03-28 Released: 2011-04-20
Deposition Author(s): Dong, A., Zeng, H., Loppnau, P., Walker, J.R., 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: 1.73 Å
R-Value Free: 0.228
R-Value Work: 0.194
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Methyltransferase domain of human PR domain-containing protein 11

Dong, A., Zeng, H., Loppnau, P., Walker, J.R., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Wu, H., Structural Genomics Consortium (SGC)

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PR domain-containing protein 11	A	237	Homo sapiens	Mutation(s): 0 Gene Names: PRDM11, PFM8 EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQV5 (Homo sapiens) Explore Q9NQV5 Go to UniProtKB: Q9NQV5
PHAROS: Q9NQV5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NQV5
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	UNKNOWN ATOM OR ION X		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.228
R-Value Work: 0.194
R-Value Observed: 0.196
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.154	α = 90
b = 55.156	β = 90
c = 106.283	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-04-20

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2011-04-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.