9GYD: Ferredoxin Wild-type -As-isolated state

Ferredoxin Wild-type -As-isolated state. Determined by X-ray diffraction at 0.92 Å resolution. Released 28 May 2025.

Method: X-ray diffraction
Resolution: 0.92 Å
Organism: Spinacia oleracea
Chains: 1
Atoms: 940
Mol. weight: 11.45 kDa
Ligands: FES
Released: 28 May 2025

Explore 9GYD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GYD contains 4 α-helices and 7 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
β-strand	12-19	8	1
α-helix	24-30	7
β-strand	48-53	6	1
β-strand	56-57	2	2
α-helix	66-70	5
β-strand	73-75	3	1
α-helix	76-78	3
β-strand	80-81	2	2
β-strand	85-88	4	1
α-helix	92-94	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ferredoxin-1, chloroplastic	A	protein	105	Spinacia oleracea	P00221 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9GYD_1 Ferredoxin-1, chloroplastic (chains A)
GPLGSPEFAAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLK
TGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA

Ligands and cofactors

ID	Name	Formula	Copies
FES	FE2/S2 (inorganic) cluster	Fe2 S2	1

Primary citation

Cyanophenylalanine as an Infrared Probe for Iron-Sulfur Cluster Redox State in Multicenter Metalloenzymes. Duan, Z., Wei, J., Carr, S.B. et al. Chembiochem (2025) 26:e202500251-e202500251. DOI 10.1002/cbic.202500251 · PubMed

Other PDB entries of the same protein (UniProt P00221 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9TXE 0.95 Å, Spinach Ferredoxin I, Oxidised
9GYN 1.0 Å, Ferredoxin Wild-type - Reduced state
9GYR 1.1 Å, Ferredoxin CNF labelled, oxidised state
9GYU 1.1 Å, Ferredoxin CNF-labelled reduced state
9TXQ 1.1 Å, Spinach Ferredoxin I, Reduced with Methyl Viologen at -450mV
29KI 1.11 Å, Spinach Ferredoxin I, Reduced, -400 mV
9GYL 1.19 Å, Ferredoxin Wild-type -Oxidised state
9TXO 1.2 Å, Spinach Ferredoxin I, Re-Oxidised
1A70 1.7 Å, Spinach ferredoxin
9HI3 1.7 Å, C-terminal domain of pectobacterial FusB in complex with spinach ferredoxin 1

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