8OF1

Structure of ALDH5F1 from moss Physcomitrium patens in complex with NAD+ in the contracted conformation

PDB DOI: https://doi.org/10.2210/pdb8OF1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Physcomitrium patens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2023-03-13 Released: 2024-03-27
Deposition Author(s): Morera, S., Kopecny, D., Vigouroux, A.
Funding Organization(s): Czech Science Foundation, Ministry of Education, Youth and Sports of the Czech Republic, Palacky University in Olomouc

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.194
R-Value Work: 0.172
R-Value Observed: 0.173

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A study on abiotic stress responses of aldehyde dehydrogenase (ALDH) superfamilies in moss and barley focused on members linked to the GABA shunt pathway

Kopecny, D.J., Belicek, J., Vigouroux, A., Luptakova, E., Koncitikova, R., von Schwartzenberg, K., Cavar Zeljkovic, S., Supikova, k., Gruz, J., Valarik, m., Bergougnoux, V., Kopecny, D., Morera, S., Kopecna, M.

To be published.

Macromolecule Content

Total Structure Weight: 113.32 kDa
Atom Count: 8,576
Modelled Residue Count: 1,007
Deposited Residue Count: 1,024
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate-semialdehyde dehydrogenase	A, B	512	Physcomitrium patens	Mutation(s): 0 Gene Names: PHYPA_030493 EC: 1.2.1.24
UniProt
Find proteins for A0A2K1ICJ7 (Physcomitrium patens) Explore A0A2K1ICJ7 Go to UniProtKB: A0A2K1ICJ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2K1ICJ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain Q [auth B] MOL2 format, chain C [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain C [auth A] mmCIF format, chain Q [auth B]	C [auth A], Q [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain Q [auth B]
P33 Query on P33 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain R [auth B] MOL2 format, chain D [auth A] MOL2 format, chain R [auth B] mmCIF format, chain D [auth A] mmCIF format, chain R [auth B]	D [auth A], R [auth B]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain R [auth B] Interactions & Density Focus chain D [auth A] Focus chain R [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain E [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain E [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	E [auth A], S [auth B], T [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain E [auth A] Focus chain S [auth B] Focus chain T [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] M [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], M [auth A], N [auth A], O [auth A], P [auth A], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], U [auth B], V [auth B], W [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.194
R-Value Work: 0.172
R-Value Observed: 0.173
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 212.505	α = 90
b = 212.505	β = 90
c = 186.74	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
BUSTER	refinement
autoPROC	data reduction
STARANISO	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-27

Deposition Author(s):

Morera, S.

Kopecny, D.

Vigouroux, A.

Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	21-07661S
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	CZ.02.1.01/0.0/0.0/16_019/0000827
Palacky University in Olomouc	Czech Republic	JG_2020_001