4RG1 | pdb_00004rg1

Methyltransferase domain of C9orf114

PDB DOI: https://doi.org/10.2210/pdb4RG1/pdb

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

Deposited: 2014-09-29 Released: 2014-10-15
Deposition Author(s): Dong, A., Zeng, H., Walker, J.R., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Wu, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.208 (Depositor), 0.214 (DCC)
R-Value Work:
0.172 (Depositor), 0.182 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The Crystal Structure of Human C9orf114 in complex with S-adenosyl-homocysteine

Zeng, H., Dong, A., Walker, J.R., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Wu, H.

To be published.

Macromolecule Content

Total Structure Weight: 75.53 kDa
Atom Count: 5,270
Modeled Residue Count: 567
Deposited Residue Count: 626
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C9orf114	A, B	313	Homo sapiens	Mutation(s): 0 Gene Names: C9orf114 EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T280 (Homo sapiens) Explore Q5T280 Go to UniProtKB: Q5T280
PHAROS: Q5T280 GTEx: ENSG00000198917
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5T280
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
15P Query on 15P Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], J [auth B], K [auth B]	POLYETHYLENE GLYCOL (N=34) C₆₉ H₁₄₀ O₃₅ VUYXVWGKCKTUMF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B]
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
PGO Query on PGO Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	S-1,2-PROPANEDIOL C₃ H₈ O₂ DNIAPMSPPWPWGF-VKHMYHEASA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.208 (Depositor), 0.214 (DCC)
R-Value Work: 0.172 (Depositor), 0.182 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.509	α = 90
b = 67.816	β = 90
c = 85.2	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-10-15

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2014-10-15
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

4RG1 | pdb_00004rg1

Methyltransferase domain of C9orf114

Literature

The Crystal Structure of Human C9orf114 in complex with S-adenosyl-homocysteine

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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