2PXX

Human putative methyltransferase MGC2408

PDB DOI: https://doi.org/10.2210/pdb2PXX/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-05-14 Released: 2007-05-22
Deposition Author(s): Tempel, W., Wu, H., Dombrovsky, L., Zeng, H., Zhu, H., Loppnau, P., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.226 (Depositor), 0.230 (DCC)
R-Value Work:
0.210 (Depositor), 0.210 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

An intact SAM-dependent methyltransferase fold is encoded by the human endothelin-converting enzyme-2 gene.

Tempel, W., Wu, H., Dombrovsky, L., Zeng, H., Loppnau, P., Zhu, H., Plotnikov, A.N., Bochkarev, A.

(2009) Proteins 74: 789-793

PubMed: 19089949 Search on PubMed
DOI: https://doi.org/10.1002/prot.22299
Primary Citation of Related Structures:
2PXX

Organizational Affiliation

Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.

Macromolecule Content

Total Structure Weight: 24.3 kDa
Atom Count: 1,830
Modelled Residue Count: 213
Deposited Residue Count: 215
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein MGC2408	A	215	Homo sapiens	Mutation(s): 1 Gene Names: MGC2408 EC: 2.1.1
UniProt
Find proteins for P0DPD7 (Homo sapiens) Explore P0DPD7 Go to UniProtKB: P0DPD7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DPD7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.226 (Depositor), 0.230 (DCC)
R-Value Work: 0.210 (Depositor), 0.210 (DCC)

Diffraction Data: https://doi.org/10.18430/m32pxx

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.883	α = 90
b = 45.56	β = 105.87
c = 55.102	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-05-22

Deposition Author(s):

Arrowsmith, C.H.

Plotnikov, A.N.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-05-22
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2021-10-20
Changes: Database references, Derived calculations
Version 1.5: 2024-02-21
Changes: Data collection

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.