7DAH | pdb_00007dah

Adenosine triphosphate phosphoribosyltransferase from Vibrio cholerae in complex with ATP and PRPP

PDB DOI: https://doi.org/10.2210/pdb7DAH/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae M66-2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-10-16 Released: 2021-10-20
Deposition Author(s): Pal, R.K., Gourinath, S., Biswal, B.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.92 Å
R-Value Free:
0.268 (Depositor), 0.264 (DCC)
R-Value Work:
0.216 (Depositor), 0.215 (DCC)
R-Value Observed:
0.219 (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

Adenosine triphosphate phosphoribosyltransferase from Vibrio cholerae in complex with ATP and PRPP

Pal, R.K., Gourinath, S., Biswal, B.K.

To be published.

Macromolecule Content

Total Structure Weight: 210.4 kDa
Atom Count: 13,159
Modeled Residue Count: 1,735
Deposited Residue Count: 1,860
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP phosphoribosyltransferase	A, B, C, D, E A, B, C, D, E, F	310	Vibrio cholerae M66-2	Mutation(s): 0 Gene Names: hisG, VCM66_1088 EC: 2.4.2.17
UniProt
Find proteins for Q9KSX4 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KSX4 Go to UniProtKB: Q9KSX4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KSX4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain Z [auth F] MOL2 format, chain M [auth C] MOL2 format, chain Z [auth F] mmCIF format, chain M [auth C] mmCIF format, chain Z [auth F]	M [auth C], Z [auth F]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain M [auth C] Focus chain Z [auth F] Interactions & Density Focus chain M [auth C] Focus chain Z [auth F]
PRP (Subject of Investigation/LOI) Query on PRP Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain Y [auth F] MOL2 format, chain N [auth C] MOL2 format, chain Y [auth F] mmCIF format, chain N [auth C] mmCIF format, chain Y [auth F]	N [auth C], Y [auth F]	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose C₅ H₁₃ O₁₄ P₃ PQGCEDQWHSBAJP-TXICZTDVSA-N		Interactions Focus chain N [auth C] Focus chain Y [auth F] Interactions & Density Focus chain N [auth C] Focus chain Y [auth F]
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain P [auth D]	G [auth A], P [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain P [auth D]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain U [auth D] MOL2 format, chain J [auth A] MOL2 format, chain U [auth D] mmCIF format, chain J [auth A] mmCIF format, chain U [auth D]	J [auth A], U [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth A] Focus chain U [auth D] Interactions & Density Focus chain J [auth A] Focus chain U [auth D]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain R [auth D] MOL2 format, chain K [auth A] MOL2 format, chain R [auth D] mmCIF format, chain K [auth A] mmCIF format, chain R [auth D]	K [auth A], R [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain R [auth D] Interactions & Density Focus chain K [auth A] Focus chain R [auth D]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain X [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F]	H [auth A] I [auth A] O [auth C] Q [auth D] S [auth D] H [auth A], I [auth A], O [auth C], Q [auth D], S [auth D], T [auth D], V [auth E], X [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain W [auth F] MOL2 format, chain L [auth C] MOL2 format, chain W [auth F] mmCIF format, chain L [auth C] mmCIF format, chain W [auth F]	L [auth C], W [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Focus chain W [auth F] Interactions & Density Focus chain L [auth C] Focus chain W [auth F]