7PN0 | pdb_00007pn0

Crystal structure of the Phosphorybosylpyrophosphate synthetase II from Thermus thermophilus at R32 space group

PDB DOI: https://doi.org/10.2210/pdb7PN0/pdb
Entry: 7PN0 supersedes: 7AWO

Classification: TRANSFERASE
Organism(s): Thermus thermophilus
Expression System: Thermus thermophilus
Mutation(s): No

Deposited: 2021-09-04 Released: 2021-09-29
Deposition Author(s): Timofeev, V.I., Abramchik, Y.A., Kostromina, M.A., Esipov, R.S., Kuranova, I.P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.221 (Depositor), 0.228 (DCC)
R-Value Work:
0.186 (Depositor), 0.195 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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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 the Phosphorybosylpyrophosphate synthetase II from Thermus thermophilus at R32 space group

Timofeev, V.I., Abramchik, Y.A., Kostromina, M.A., Esipov, R.S., Kuranova, I.P.

To be published.

Macromolecule Content

Total Structure Weight: 70.35 kDa
Atom Count: 5,097
Modeled Residue Count: 620
Deposited Residue Count: 632
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose-phosphate pyrophosphokinase	A, B	316	Thermus thermophilus	Mutation(s): 0 Gene Names: prs, HB27c_C1311 EC: 2.7.6.1
UniProt
Find proteins for Q5SHU3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHU3 Go to UniProtKB: Q5SHU3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHU3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth B] D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], J [auth B], K [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]