9I07 | pdb_00009i07

Photosynthetic A8B8 glycerldeyde-3-phosphate dehydrogenase hexadecamer (major conformer) from Spinacia oleracea.

PDB DOI: https://doi.org/10.2210/pdb9I07/pdb
EM Map EMD-52553: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Spinacia oleracea
Mutation(s): No

Deposited: 2025-01-14 Released: 2026-01-21
Deposition Author(s): Marotta, R., Fermani, S., Sparla, F.
Funding Organization(s): iNEXT-Discovery

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Photosynthetic A8B8 glycerldeyde-3-phosphate dehydrogenase hexadecamer (major conformer) from Spinacia oleracea.

Marotta, R., Fermani, S., Sparla, F.

To be published.

Macromolecule Content

Total Structure Weight: 615.9 kDa
Atom Count: 43,184
Modeled Residue Count: 5,640
Deposited Residue Count: 5,640
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic	A [auth O] C [auth Q] E [auth A] G [auth C] I [auth E] A [auth O], C [auth Q], E [auth A], G [auth C], I [auth E], K [auth G], M [auth I], O [auth K]	368	Spinacia oleracea	Mutation(s): 0 EC: 1.2.1.13
UniProt
Find proteins for P12860 (Spinacia oleracea) Explore P12860 Go to UniProtKB: P12860
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12860
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic	B [auth P] D [auth R] F [auth B] H [auth D] J [auth F] B [auth P], D [auth R], F [auth B], H [auth D], J [auth F], L [auth H], N [auth J], P [auth L]	337	Spinacia oleracea	Mutation(s): 0 EC: 1.2.1.13
UniProt
Find proteins for P19866 (Spinacia oleracea) Explore P19866 Go to UniProtKB: P19866
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19866
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 AA [auth G] SDF format, chain BA [auth H] SDF format, chain CA [auth I] SDF format, chain DA [auth J] SDF format, chain EA [auth K] SDF format, chain FA [auth L] SDF format, chain Q [auth O] SDF format, chain R [auth P] SDF format, chain S [auth Q] SDF format, chain W [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth F] SDF format, chain V [auth B] SDF format, chain U [auth A] SDF format, chain T [auth R] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain CA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain EA [auth K] MOL2 format, chain FA [auth L] MOL2 format, chain Q [auth O] MOL2 format, chain R [auth P] MOL2 format, chain S [auth Q] MOL2 format, chain W [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain V [auth B] MOL2 format, chain U [auth A] MOL2 format, chain T [auth R] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain CA [auth I] mmCIF format, chain DA [auth J] mmCIF format, chain EA [auth K] mmCIF format, chain FA [auth L] mmCIF format, chain Q [auth O] mmCIF format, chain R [auth P] mmCIF format, chain S [auth Q] mmCIF format, chain W [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth F] mmCIF format, chain V [auth B] mmCIF format, chain U [auth A] mmCIF format, chain T [auth R]	AA [auth G] BA [auth H] CA [auth I] DA [auth J] EA [auth K] AA [auth G], BA [auth H], CA [auth I], DA [auth J], EA [auth K], FA [auth L], Q [auth O], R [auth P], S [auth Q], T [auth R], U [auth A], V [auth B], W [auth C], X [auth D], Y [auth E], Z [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain Q [auth O] Focus chain R [auth P] Focus chain S [auth Q] Focus chain T [auth R] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain Q [auth O] Focus chain R [auth P] Focus chain S [auth Q] Focus chain T [auth R] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F]