2B25

Human putative tRNA(1-methyladenosine)methyltransferase

PDB DOI: https://doi.org/10.2210/pdb2B25/pdb

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

Deposited: 2005-09-16 Released: 2005-09-27
Deposition Author(s): Tempel, W., Wu, H., Dong, A., Zeng, H., Loppnau, P., Arrowsmith, C., Edwards, A., Sundstrom, M., Weigelt, J., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.282 (Depositor), 0.240 (DCC)
R-Value Work:
0.247 (Depositor), 0.250 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Human putative tRNA(1-methyladenosine)methyltransferase

Wu, H., Tempel, W., Dong, A., Zeng, H., Loppnau, P., Arrowsmith, C., Edwards, A., Weigelt, J., Sundstrom, M., Bochkarev, A., Plotnikov, A.N.

To be published.

Macromolecule Content

Total Structure Weight: 76.32 kDa
Atom Count: 3,835
Modelled Residue Count: 493
Deposited Residue Count: 672
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein	A, B	336	Homo sapiens	Mutation(s): 0 EC: 2.1.1.220 (UniProt), 2.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVS5 (Homo sapiens) Explore Q9BVS5 Go to UniProtKB: Q9BVS5
PHAROS: Q9BVS5 GTEx: ENSG00000171103
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BVS5
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth A], G [auth B], H [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.282 (Depositor), 0.240 (DCC)
R-Value Work: 0.247 (Depositor), 0.250 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.533	α = 90
b = 157.106	β = 90
c = 113.492	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-09-27

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2005-09-27
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description