3w5u

Cross-linked complex between Ferredoxin and Ferredoxin-NADP+ reductase

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ferredoxin

Zea mays

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ferredoxin-1, chloroplastic × 1 （P27787） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ferredoxin-1, chloroplastic × 1 （P27787） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ferredoxin-1, chloroplastic × 1 （P27787） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Ferredoxin-1, chloroplastic × 1 （P27787） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9SLP6_MAIZE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–314； UniProt 42–355 Author chain C； PDBConstruct 1–314； UniProt 42–355 Author chain E； PDBConstruct 1–314； UniProt 42–355 Author chain G； PDBConstruct 1–314； UniProt 42–355

Ferredoxin-1, chloroplastic

Zea mays

UniProt P27787

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ferredoxin × 1 （Q9SLP6） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ferredoxin × 1 （Q9SLP6） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ferredoxin × 1 （Q9SLP6） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Ferredoxin × 1 （Q9SLP6） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FER1_MAIZE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–98； UniProt 53–150 Author chain D； PDBConstruct 1–98； UniProt 53–150 Author chain F； PDBConstruct 1–98； UniProt 53–150 Author chain H； PDBConstruct 1–98； UniProt 53–150

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3w5u
Deposition date deposition_date	2013-02-06
Structure title title	Cross-linked complex between Ferredoxin and Ferredoxin-NADP+ reductase
Keywords keywords	electron transfer complex, ELECTRON TRANSPORT; ELECTRON TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3w5u__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3w5u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3w5u__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	25.02 Å
Rg (electron density)	24.06 Å
Total Rg	24.82 Å
Atom count	3102
Residues	388
Excluded volume	55054 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3w5u__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3w5u__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3w5u__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3w5u__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Ferredoxin
Molecular weight formula_weight	35334.5 kDa
Mutation mutation	E19C
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	12485

IRAQASAVEAPATAKAKKCSKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPHKVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVSREQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRGDQWNVEVY

Source Source

Source organism organism	Zea mays
Common name common_name	maize
NCBI taxonomy ID ncbi_taxonomy_id	4577
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ferredoxin-1, chloroplastic
Molecular weight formula_weight	10534.4 kDa
Mutation mutation	S59C
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQCDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA

Source Source

Source organism organism	Zea mays
Common name common_name	maize
NCBI taxonomy ID ncbi_taxonomy_id	4577
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	33

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3w5ua1
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.4 — Riboflavin synthase domain-like
Family Family family	b.43.4.0 — automated matches

Domain ID domain_id	d3w5ua2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamily	c.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family family	c.25.1.0 — automated matches

Domain ID domain_id	d3w5ub_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.1 — 2Fe-2S ferredoxin-related

Domain ID domain_id	d3w5uc1
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.4 — Riboflavin synthase domain-like
Family Family family	b.43.4.0 — automated matches

Domain ID domain_id	d3w5uc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamily	c.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family family	c.25.1.0 — automated matches

Domain ID domain_id	d3w5ud_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.1 — 2Fe-2S ferredoxin-related

Domain ID domain_id	d3w5ue1
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.4 — Riboflavin synthase domain-like
Family Family family	b.43.4.0 — automated matches

Domain ID domain_id	d3w5ue2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamily	c.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family family	c.25.1.0 — automated matches

Domain ID domain_id	d3w5uf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.1 — 2Fe-2S ferredoxin-related

Domain ID domain_id	d3w5ug1
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.4 — Riboflavin synthase domain-like
Family Family family	b.43.4.0 — automated matches

Domain ID domain_id	d3w5ug2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamily	c.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family family	c.25.1.0 — automated matches

Domain ID domain_id	d3w5uh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.1 — 2Fe-2S ferredoxin-related

CATH v4.4 (12 domains)

Domain ID domain_id	3w5uA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	3w5uA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

Domain ID domain_id	3w5uB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	30 — Beta-grasp domain

Domain ID domain_id	3w5uC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	3w5uC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

Domain ID domain_id	3w5uD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	30 — Beta-grasp domain

Domain ID domain_id	3w5uE01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	3w5uE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

Domain ID domain_id	3w5uF00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	30 — Beta-grasp domain

Domain ID domain_id	3w5uG01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	3w5uG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

Domain ID domain_id	3w5uH00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	30 — Beta-grasp domain

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Unit-cell length a length_a	59.202 Å
Unit-cell length b length_b	153.634 Å
Unit-cell length c length_c	100.107 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.42 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	45.460 Å
R factor r_factor	0.2290
R_work r_work	0.2263
R_free r_free	0.2797

Cross-linked complex between Ferredoxin and Ferredoxin-NADP+ reductase

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ferredoxin

State in the Current Structure

Other States of the Same Protein in the Database

Ferredoxin-1, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3w5u__assembly_1__model_1

3w5u__assembly_1__model_1 | I(q)

3w5u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Cross-linked complex between Ferredoxin and Ferredoxin-NADP+ reductase

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ferredoxin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ferredoxin-1, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3w5u__assembly_1__model_1

3w5u__assembly_1__model_1 | I(q)

3w5u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)