1EFH

CRYSTAL STRUCTURE OF THE HUMAN HYDROXYSTEROID SULFOTRANSFERASE IN THE PRESENCE OF PAP

PDB DOI: https://doi.org/10.2210/pdb1EFH/pdb

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

Deposited: 2000-02-08 Released: 2000-09-06
Deposition Author(s): Pedersen, L.C., Petrotchenko, E.V., Negishi, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.239
R-Value Work: 0.202
R-Value Observed: 0.204

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 SULT2A3, human hydroxysteroid sulfotransferase.

Pedersen, L.C., Petrotchenko, E.V., Negishi, M.

(2000) FEBS Lett 475: 61-64

PubMed: 10854859 Search on PubMed
DOI: https://doi.org/10.1016/s0014-5793(00)01479-4
Primary Citation of Related Structures:
1EFH

PubMed Abstract:
The crystal structure of SULT2A3 human hydroxysteroid sulfotransferase has been solved at 2.4 A resolution in the presence of 3'-phosphoadenosine 5'-phosphate (PAP). The overall structure is similar to those of SULT1 enzymes such as estrogen sulfotransferase and the PAP binding site is conserved, however, significant differences exist in the positions of loops Pro14-Ser20, Glu79-Ile82 and Tyr234-Gln244 in the substrate binding pocket. Moreover, protein interaction in the crystal structure has revealed a possible dimer-directed conformational alteration that may regulate the SULT activity.

Organizational Affiliation

Pharmacogenetics Section, Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.

Macromolecule Content

Total Structure Weight: 69.95 kDa
Atom Count: 4,842
Modelled Residue Count: 563
Deposited Residue Count: 584
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYDROXYSTEROID SULFOTRANSFERASE	A, B	292	Homo sapiens	Mutation(s): 0 Gene Names: CDNA LIBRARY EC: 2.8.2.2 (PDB Primary Data), 2.8.2.14 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q06520 (Homo sapiens) Explore Q06520 Go to UniProtKB: Q06520
PHAROS: Q06520 GTEx: ENSG00000105398
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q06520
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A3P Query on A3P Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	ADENOSINE-3'-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ WHTCPDAXWFLDIH-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.239
R-Value Work: 0.202
R-Value Observed: 0.204
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.19	α = 90
b = 96.82	β = 90
c = 127.38	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2000-09-06

Deposition Author(s):

Pedersen, L.C.

Petrotchenko, E.V.

Negishi, M.

Revision History (Full details and data files)

Version 1.0: 2000-09-06
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-06-06
Changes: Data collection, Derived calculations
Version 1.4: 2024-02-07
Changes: Data collection, Database references, Derived calculations