9GYR: Ferredoxin CNF labelled, oxidised state

Ferredoxin CNF labelled, oxidised state. Determined by X-ray diffraction at 1.1 Å resolution. Released 28 May 2025.

Method: X-ray diffraction
Resolution: 1.1 Å
Organism: Spinacia oleracea
Chains: 4
Atoms: 3,858
Mol. weight: 45.83 kDa
Ligands: FES
Released: 28 May 2025

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

Secondary structure: helices and β-sheets

9GYR contains 13 α-helices and 28 β-strands across 4 chains. 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.

Chains A and C: 3 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
β-strand	80-81	2	2
β-strand	85-88	4	1
α-helix	92-94	3

Chain B: 3 helices, 7 β-strands

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

Chain D: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	7
β-strand	12-19	8	7
α-helix	24-30	7
β-strand	48-53	6	7
β-strand	56-57	2	8
α-helix	66-70	5
β-strand	73-75	3	7
α-helix	76-78	3
β-strand	80-81	2	8
β-strand	85-88	4	7
α-helix	92-95	4

Molecules and chains

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

Sequence of entity 1 (A, B, C, D), FASTA

>9GYR_1 Ferredoxin-1, chloroplastic (chains A, B, C, D)
GPLGSPEFAAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPFSCRAGSCSSCAGKLK
TGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA

Ligands and cofactors

ID	Name	Formula	Copies
FES	FE2/S2 (inorganic) cluster	Fe2 S2	4

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:

9GYD 0.92 Å, Ferredoxin Wild-type -As-isolated state
9TXE 0.95 Å, Spinach Ferredoxin I, Oxidised
9GYN 1.0 Å, Ferredoxin Wild-type - Reduced 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

Browse structure collections

About this viewer

MolViewer shows 9GYR directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.