4XCX | pdb_00004xcx

METHYLTRANSFERASE DOMAIN OF SMALL RNA 2'-O-METHYLTRANSFERASE

PDB DOI: https://doi.org/10.2210/pdb4XCX/pdb

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

Deposited: 2014-12-18 Released: 2015-01-14
Deposition Author(s): Walker, J.R., Zeng, H., Dong, A., Li, Y., Wernimont, A., 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: 2.84 Å
R-Value Free:
0.249 (Depositor), 0.242 (DCC)
R-Value Work:
0.225 (Depositor), 0.226 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of human C1ORF59 in complex with SAH

Walker, J.R., Zeng, H., Dong, A., Li, Y., Wernimont, A., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Wu, H., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 28.73 kDa
Atom Count: 1,733
Modeled Residue Count: 216
Deposited Residue Count: 249
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Small RNA 2'-O-methyltransferase	A	249	Homo sapiens	Mutation(s): 0 Gene Names: HENMT1, C1orf59 EC: 2.1.1 (PDB Primary Data), 2.1.1.386 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T8I9 (Homo sapiens) Explore Q5T8I9 Go to UniProtKB: Q5T8I9
PHAROS: Q5T8I9 GTEx: ENSG00000162639
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5T8I9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free: 0.249 (Depositor), 0.242 (DCC)
R-Value Work: 0.225 (Depositor), 0.226 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.025	α = 90
b = 166.025	β = 90
c = 74.478	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data reduction
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-3000	data scaling
BALBES	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-01-14

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2015-01-14
Type: Initial release
Version 1.1: 2015-02-11
Changes: Database references
Version 1.2: 2015-02-25
Changes: Database references
Version 1.3: 2018-01-24
Changes: Database references, Derived calculations, Source and taxonomy, Structure summary
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Refinement description