7DAH

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
R-Value Work: 0.216
R-Value Observed: 0.219

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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]	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]	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]	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]	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]	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]	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]	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]