3AP2 | pdb_00003ap2

Crystal structure of human tyrosylprotein sulfotransferase-2 complexed with PAP,C4 peptide, and phosphate ion

PDB DOI: https://doi.org/10.2210/pdb3AP2/pdb

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

Deposited: 2010-10-09 Released: 2011-10-26
Deposition Author(s): Teramoto, T., Fujikawa, Y., Kawaguchi, Y., Kurogi, K., Soejima, M., Adachi, R., Nakanishi, Y., Mishiro-Sato, E., Liu, M.-C., Sakakibara, Y., Suiko, M., Kimura, M., Kakuta, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.249 (Depositor), 0.243 (DCC)
R-Value Work:
0.207 (Depositor), 0.203 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of human tyrosylprotein sulfotransferase-2: Insights into substrate-binding and catalysis of post-translational protein tyrosine sulfation

Teramoto, T., Fujikawa, Y., Kawaguchi, Y., Kurogi, K., Soejima, M., Adachi, R., Nakanishi, Y., Mishiro-Sato, E., Liu, M.-C., Sakakibara, Y., Suiko, M., Kimura, M., Kakuta, Y.

To be published.

Macromolecule Content

Total Structure Weight: 78.95 kDa
Atom Count: 5,089
Modeled Residue Count: 615
Deposited Residue Count: 692
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-tyrosine sulfotransferase 2	A, B	337	Homo sapiens	Mutation(s): 0 Gene Names: TPST2 EC: 2.8.2.20
UniProt & NIH Common Fund Data Resources
Find proteins for O60704 (Homo sapiens) Explore O60704 Go to UniProtKB: O60704
PHAROS: O60704 GTEx: ENSG00000128294
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60704
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C4 peptide	C [auth S], D [auth T]	9	N/A	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A3P Query on A3P Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B]	ADENOSINE-3'-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ WHTCPDAXWFLDIH-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth T] MOL2 format, chain H [auth T] mmCIF format, chain H [auth T]	H [auth T]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth T] Interactions & Density Focus chain H [auth T]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.249 (Depositor), 0.243 (DCC)
R-Value Work: 0.207 (Depositor), 0.203 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.379	α = 90
b = 138.379	β = 90
c = 228.547	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-10-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-10-26
Type: Initial release
Version 1.1: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary