3BGV

Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with SAH

PDB DOI: https://doi.org/10.2210/pdb3BGV/pdb

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

Deposited: 2007-11-27 Released: 2007-12-04
Deposition Author(s): Lunin, V.V., Wu, H., Zeng, H., Antoshenko, T., MacKenzie, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Plotnikov, A.N., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.294
R-Value Work: 0.221
R-Value Observed: 0.225

Starting Model: experimental
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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 RNA (guanine-7-) methyltransferase in complex with SAH.

Wu, H., Lunin, V.V., Zeng, H., Antoshenko, T., MacKenzie, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Plotnikov, A.N.

To be published.

Macromolecule Content

Total Structure Weight: 148.63 kDa
Atom Count: 9,359
Modelled Residue Count: 1,078
Deposited Residue Count: 1,252
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA cap guanine-N7 methyltransferase	A, B, C, D	313	Homo sapiens	Mutation(s): 0 Gene Names: RNMT, KIAA0398 EC: 2.1.1.56
UniProt & NIH Common Fund Data Resources
Find proteins for O43148 (Homo sapiens) Explore O43148 Go to UniProtKB: O43148
PHAROS: O43148 GTEx: ENSG00000101654
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43148
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 E [auth C] SDF format, chain F [auth C] SDF format, chain G [auth C] SDF format, chain H [auth C] MOL2 format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C] mmCIF format, chain E [auth C] mmCIF format, chain F [auth C] mmCIF format, chain G [auth C] mmCIF format, chain H [auth C]	E [auth C], F [auth C], G [auth C], H [auth C]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Interactions & Density Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.294
R-Value Work: 0.221
R-Value Observed: 0.225
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.787	α = 90
b = 99.672	β = 90
c = 167.782	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-12-04

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-12-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3BGV

Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with SAH

The crystal structure of human RNA (guanine-7-) methyltransferase in complex with SAH.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)