8OFM | pdb_00008ofm

Structure of the ALDEHYDE DEHYDROGENASE 5F1 (ALDH5F1) from the moss Physcomitrium patens in complex with NAD in an extended conformation

PDB DOI: https://doi.org/10.2210/pdb8OFM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Physcomitrium patens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-03-16 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, Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.196 (Depositor), 0.180 (DCC)
R-Value Work:
0.173 (Depositor), 0.161 (DCC)
R-Value Observed:
0.174 (Depositor)

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, D., 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: 113.65 kDa
Atom Count: 8,571
Modeled Residue Count: 1,007
Deposited Residue Count: 1,024
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2K1ICJ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 V [auth B] SDF format, chain H [auth A] MOL2 format, chain V [auth B] MOL2 format, chain H [auth A] mmCIF format, chain V [auth B] mmCIF format, chain H [auth A]	H [auth A], V [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain H [auth A] Focus chain V [auth B] Interactions & Density Focus chain H [auth A] Focus chain V [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain IA [auth B] SDF format, chain I [auth A] SDF format, chain HA [auth B] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B]	BA [auth B] CA [auth B] DA [auth B] EA [auth B] FA [auth B] BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], I [auth A], IA [auth B], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain KA [auth B] SDF format, chain JA [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain AA [auth B]	AA [auth B] D [auth A] E [auth A] F [auth A] G [auth A] AA [auth B], D [auth A], E [auth A], F [auth A], G [auth A], JA [auth B], KA [auth B], T [auth A], U [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain C [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain C [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain C [auth A]	C [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain C [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.196 (Depositor), 0.180 (DCC)
R-Value Work: 0.173 (Depositor), 0.161 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 212.309	α = 90
b = 212.309	β = 90
c = 187.344	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

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
Other government		JG_2020_001