9I06 | pdb_00009i06

Photosynthetic A8B8 glyceraldehyde-3-phosphate dehydrogenase (minor conformer) from Spinacia oleracea.

PDB DOI: https://doi.org/10.2210/pdb9I06/pdb
EM Map EMD-52552: 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: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Photosynthetic A8B8 glyceraldehyde-3-phosphate dehydrogenase (minor 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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic	A C E G I A, C, E, G, I, K, M [auth O], O [auth Q]	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12860
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic	B D F H J B, D, F, H, J, L, N [auth P], P [auth R]	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 BA [auth L] SDF format, chain U [auth E] SDF format, chain W [auth G] SDF format, chain X [auth H] SDF format, chain Y [auth I] SDF format, chain Z [auth J] SDF format, chain V [auth F] SDF format, chain T [auth D] SDF format, chain S [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth A] SDF format, chain FA [auth R] SDF format, chain EA [auth Q] SDF format, chain DA [auth P] SDF format, chain CA [auth O] SDF format, chain AA [auth K] MOL2 format, chain BA [auth L] MOL2 format, chain U [auth E] MOL2 format, chain W [auth G] MOL2 format, chain X [auth H] MOL2 format, chain Y [auth I] MOL2 format, chain Z [auth J] MOL2 format, chain V [auth F] MOL2 format, chain T [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain FA [auth R] MOL2 format, chain EA [auth Q] MOL2 format, chain DA [auth P] MOL2 format, chain CA [auth O] MOL2 format, chain AA [auth K] mmCIF format, chain BA [auth L] mmCIF format, chain U [auth E] mmCIF format, chain W [auth G] mmCIF format, chain X [auth H] mmCIF format, chain Y [auth I] mmCIF format, chain Z [auth J] mmCIF format, chain V [auth F] mmCIF format, chain T [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain FA [auth R] mmCIF format, chain EA [auth Q] mmCIF format, chain DA [auth P] mmCIF format, chain CA [auth O] mmCIF format, chain AA [auth K]	AA [auth K] BA [auth L] CA [auth O] DA [auth P] EA [auth Q] AA [auth K], BA [auth L], CA [auth O], DA [auth P], EA [auth Q], FA [auth R], Q [auth A], R [auth B], S [auth C], T [auth D], U [auth E], V [auth F], W [auth G], X [auth H], Y [auth I], Z [auth J]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth O] Focus chain DA [auth P] Focus chain EA [auth Q] Focus chain FA [auth R] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth O] Focus chain DA [auth P] Focus chain EA [auth Q] Focus chain FA [auth R] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J]