6XI5 | pdb_00006xi5

Crystal structure of human N-acetylserotonin O-methyltransferase-like protein soaked with PDHPTAO

PDB DOI: https://doi.org/10.2210/pdb6XI5/pdb

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

Deposited: 2020-06-19 Released: 2021-06-23
Deposition Author(s): Stogios, P.J., Evdokimova, E., Yakunin, A., Savchenko, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free:
0.293 (Depositor), 0.291 (DCC)
R-Value Work:
0.241 (Depositor), 0.243 (DCC)
R-Value Observed:
0.243 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of human N-acetylserotonin O-methyltransferase-like protein soaked with PDHPTAO

Yakunin, A.

To be published.

Macromolecule Content

Total Structure Weight: 51.83 kDa
Atom Count: 3,254
Modeled Residue Count: 408
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable bifunctional dTTP/UTP pyrophosphatase/methyltransferase protein	A, B	230	Homo sapiens	Mutation(s): 0 Gene Names: ASMTL EC: 3.6.1.9 (PDB Primary Data), 2.1.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O95671 (Homo sapiens) Explore O95671 Go to UniProtKB: O95671
PHAROS: O95671 GTEx: ENSG00000169093
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O95671
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.293 (Depositor), 0.291 (DCC)
R-Value Work: 0.241 (Depositor), 0.243 (DCC)
R-Value Observed: 0.243 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.733	α = 90
b = 82.86	β = 90
c = 117.232	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
PHENIX	model building
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-06-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-06-23
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.