9L1I | pdb_00009l1i

Crystal structure of PpRib7 in complex with NADPH (P212121 form)

PDB DOI: https://doi.org/10.2210/pdb9L1I/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Komagataella pastoris
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-12-14 Released: 2025-12-17
Deposition Author(s): Chen, S.C.
Funding Organization(s): National Science Council (NSC, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.253 (Depositor), 0.252 (DCC)
R-Value Work:
0.199 (Depositor), 0.199 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Divergence of RibG/Rib7 reductases in riboflavin biosynthesis: A study of Pichia pastoris Rib7 reductase

Chen, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 56.9 kDa
Atom Count: 3,998
Modeled Residue Count: 486
Deposited Residue Count: 502
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase	A, B	251	Komagataella pastoris	Mutation(s): 0 Gene Names: RIB7, PP7435_Chr3-1080 EC: 1.1.1.302
UniProt
Find proteins for F2QX95 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)) Explore F2QX95 Go to UniProtKB: F2QX95
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F2QX95
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.253 (Depositor), 0.252 (DCC)
R-Value Work: 0.199 (Depositor), 0.199 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.217	α = 90
b = 79.439	β = 90
c = 139.165	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Council (NSC, Taiwan)	Taiwan	NSTC 113 2311 B 992 001

Revision History (Full details and data files)

Version 1.0: 2025-12-17
Type: Initial release

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.