9R1S | pdb_00009r1s

Crystal structure of an NtA622L variant in complex with NADPH and Nicotinic acid N-glucoside

PDB DOI: https://doi.org/10.2210/pdb9R1S/pdb

Classification: PLANT PROTEIN
Organism(s): Nicotiana tabacum
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-04-28 Released: 2026-05-06
Deposition Author(s): Mokos, D., Daniel, B.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.242 (Depositor), 0.249 (DCC)
R-Value Work:
0.199 (Depositor), 0.214 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

A622: A key oxidoreductase in the Nicotine biosynthesis

Mokos, D., Leitner, D., Schruefer, A., Grubmueller, S., Reisz, C., Juric, J., Berger, T., Singh, A., Friess, M., Breinbauer, R., Gruber, K., Daniel, B.

To be published.

Macromolecule Content

Total Structure Weight: 35.67 kDa
Atom Count: 2,703
Modeled Residue Count: 306
Deposited Residue Count: 310
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoflavone reductase homolog A622-like	A	310	Nicotiana tabacum	Mutation(s): 3 Gene Names: A622L, IRL2 EC: 1.3.1
UniProt
Find proteins for B6VRE6 (Nicotiana tabacum) Explore B6VRE6 Go to UniProtKB: B6VRE6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B6VRE6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
A1JBN (Subject of Investigation/LOI) Query on A1JBN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-(beta-D-glucosyl)nicotinate C₁₂ H₁₆ N O₇ CRXJVFIHZPTDKA-KAMPLNKDSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.242 (Depositor), 0.249 (DCC)
R-Value Work: 0.199 (Depositor), 0.214 (DCC)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.697	α = 110.028
b = 45.076	β = 94.801
c = 46.471	γ = 112.579

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	P34337
Austrian Science Fund	Austria	DOC46
Austrian Science Fund	Austria	DOC130

Revision History (Full details and data files)

Version 1.0: 2026-05-06
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.