SAXSdb — 5efw

▼

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

NPH1-1

Avena sativa

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 404–546	Fragment：UNP residues 404-546 Mutation：C450A	Z-dark, a small protein based on the Z domain affibody × 2 FMN FLAVIN MONONUCLEOTIDE × 1 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 3.5；293.15 K；2 M ammonium sulfate, 0.1 M sodium citrate pH 3.5	Resolution 2.10 Å R-free 0.257

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5EFW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2V0U n- and c-terminal helices of oat lov2 (404-546) are involved in light-induced signal transduction (cryo dark structure of lov2 (404-546)) Deposited 2007-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 404–546（143 aa） Fragment：LIGHT, OXYGEN, VOLTAGE DOMAIN, RESIDUES 404-546	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 GOL GLYCEROL × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.40 Å R-free 0.197
2V0W N- and C-terminal helices of oat LOV2 (404-546) are involved in light- induced signal transduction (cryo-trapped light structure of LOV2 (404-546)) Deposited 2007-05-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 404–546（143 aa） Fragment：LIGHT, OXYGEN, VOLTAGE DOMAIN, RESIDUES 404-546	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；Reservoir: 0.07 M sodium acetate, pH 4.6, 5.6% PEG 4000, 30% glycerol	Resolution 1.70 Å R-free 0.215
2V1A N- and C-terminal helices of oat LOV2 (404-546) are involved in light-induced signal transduction (room temperature (293K) dark structure of LOV2 (404-546)) Deposited 2007-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 404–546（143 aa） Fragment：LIGHT, OXYGEN, VOLTAGE DOMAIN, RESIDUES 404-546	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP	Resolution 1.65 Å R-free 0.195
2V1B N- and C-terminal helices of oat LOV2 (404-546) are involved in light-induced signal transduction (room temperature (293K) light structure of LOV2 (404-546)) Deposited 2007-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 404–546（143 aa） Fragment：LIGHT, OXYGEN, VOLTAGE DOMAIN, RESIDUES 404-546	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.55 Å R-free 0.212
2WKP Structure of a photoactivatable Rac1 containing Lov2 Wildtype Deposited 2009-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 404–546（143 aa） Fragment：NPH1-1, RESIDUES 404-546 AND P21-RAC1, RESIDUES 4-180	Mutation：YES	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 FMN FLAVIN MONONUCLEOTIDE × 1 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 100 MM CA ACETATE, 100 MM SODIUM CACODYLATE PH 5.5, 12 % (W/V) PEG 8000	Resolution 1.90 Å R-free 0.195
2WKQ Structure of a photoactivatable Rac1 containing the Lov2 C450A Mutant Deposited 2009-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 404–546（143 aa） Fragment：NPH1-1 RESIDUES 404-546 AND P21-RAC1, RESIDUES 4-180	Mutation：YES	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 FMN FLAVIN MONONUCLEOTIDE × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions 100 MM POTASSIUM CHLORIDE, 5% (W/V) PEG 4000	Resolution 1.60 Å R-free 0.186
2WKR Structure of a photoactivatable Rac1 containing the Lov2 C450M Mutant Deposited 2009-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 404–546（143 aa） Fragment：NPH1-1, RESIDUES 404-546 AND P21-RAC1, RESIDUES 4-180	Mutation：YES	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 FMN FLAVIN MONONUCLEOTIDE × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions 18 % (V/V) PEG 600	Resolution 2.20 Å R-free 0.226
4WF0 Crystal Structure of iLID - an Improved Light-Inducible Dimer Deposited 2014-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 404–543（140 aa） Fragment：UNP residues 405-543	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Grown in dark for 3 days. Conditions: 100mM TRIS:HCl pH 8.5, 800mM Lithium Chloride, 32% PEG 4000	Resolution 1.95 Å R-free 0.244
4WF0 Crystal Structure of iLID - an Improved Light-Inducible Dimer Deposited 2014-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 404–543（140 aa） Fragment：UNP residues 405-543	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Grown in dark for 3 days. Conditions: 100mM TRIS:HCl pH 8.5, 800mM Lithium Chloride, 32% PEG 4000	Resolution 1.95 Å R-free 0.244
5HZH Crystal structure of photoinhibitable Rac1 containing C450A mutant LOV2 domain Deposited 2016-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 404–546（143 aa）	Mutation：Q61L,Q61L,Q61L,Q61L,Q61L,Q61L,Q61L,Q61L,Q61L	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 FMN FLAVIN MONONUCLEOTIDE × 1 MG MAGNESIUM ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.2 M calcium acetate, 26% (w/v) PEG 3350	Resolution 2.60 Å R-free 0.255
5HZI Crystal structure of photoinhibitable Intersectin1 containing C450M mutant LOV2 domain Deposited 2016-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 404–546（143 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.5, 9% (w/v) PEG 8000, 9% (v/v) ethylene glycol	Resolution 2.60 Å R-free 0.285
5HZI Crystal structure of photoinhibitable Intersectin1 containing C450M mutant LOV2 domain Deposited 2016-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 404–546（143 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.5, 9% (w/v) PEG 8000, 9% (v/v) ethylene glycol	Resolution 2.60 Å R-free 0.285
5HZJ Crystal structure of photoinhibitable Intersectin1 containing wildtype LOV2 domain Deposited 2016-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 404–546（143 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.5, 9% (w/v) PEG 8000, 9% (v/v) ethylene glycol	Resolution 2.60 Å R-free 0.281
5HZJ Crystal structure of photoinhibitable Intersectin1 containing wildtype LOV2 domain Deposited 2016-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 404–546（143 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.5, 9% (w/v) PEG 8000, 9% (v/v) ethylene glycol	Resolution 2.60 Å R-free 0.281
5HZK Crystal structure of photoinhibitable Intersectin1 containing wildtype LOV2 domain in complex with Cdc42 Deposited 2016-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 404–546（143 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；0.1 M MES, 20% (w/v) PEG 6000	Resolution 3.30 Å R-free 0.257
5HZK Crystal structure of photoinhibitable Intersectin1 containing wildtype LOV2 domain in complex with Cdc42 Deposited 2016-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 404–546（143 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；0.1 M MES, 20% (w/v) PEG 6000	Resolution 3.30 Å R-free 0.257
6NTP PTP1B Domain of PTP1B-LOV2 Chimera Deposited 2019-01-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 407–546（140 aa） Fragment：residues 2-282	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；100 mM HEPES, 200 mM magnesium acetate, and 14% polyethylene glycol 8000, pH 7.5	Resolution 1.89 Å R-free 0.212
6NTP PTP1B Domain of PTP1B-LOV2 Chimera Deposited 2019-01-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 407–546（140 aa） Fragment：residues 2-282	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；100 mM HEPES, 200 mM magnesium acetate, and 14% polyethylene glycol 8000, pH 7.5	Resolution 1.89 Å R-free 0.212
7PGX Structure of dark-adapted AsLOV2 wild type Deposited 2021-08-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 404–546（143 aa）	Not recorded	CA CALCIUM ION × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 10 PEG DI(HYDROXYETHYL)ETHER × 2 EDO 1,2-ETHANEDIOL × 2 ACT ACETATE ION × 1 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；295 K；0.1 M sodium acetate pH 4.6-5.0, 6-8% (w/v) PEG 4000, 30% (v/v) glycerol	Resolution 1.00 Å R-free 0.147
7PGY Structure of light-adapted AsLOV2 wild type Deposited 2021-08-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 404–546（143 aa）	Not recorded	CA CALCIUM ION × 2 CL CHLORIDE ION × 2 GOL GLYCEROL × 7 ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 1 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；298 K；0.1 M sodium acetate pH 4.6-5.0, 6-8% (w/v) PEG 4000, 30% (v/v) glycerol	Resolution 1.09 Å R-free 0.161
7PGZ Structure of dark-adapted AsLOV2 Q513L Deposited 2021-08-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 404–546（143 aa）	Mutation：Q513L	MG MAGNESIUM ION × 2 GOL GLYCEROL × 13 EDO 1,2-ETHANEDIOL × 2 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；0.1 M sodium acetate pH 4.6-5.0, 6-8% (w/v) PEG 4000, 30% (v/v) glycerol	Resolution 0.90 Å R-free 0.139
7PH0 Structure of light-adapted AsLOV2 Q513L Deposited 2021-08-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 404–546（143 aa）	Not recorded	CL CHLORIDE ION × 1 FMN FLAVIN MONONUCLEOTIDE × 1 GOL GLYCEROL × 3 EDO 1,2-ETHANEDIOL × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；0.1 M sodium acetate pH 4.6-5.0, 6-8% (w/v) PEG 4000, 30% (v/v) glycerol	Resolution 0.98 Å R-free 0.136

17 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	O49003_AVESA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–145； UniProt 404–546

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5efw
Deposition date deposition_date	2015-10-26
Structure title title	Crystal structure of LOV2-Zdk1 - the complex of oat LOV2 and the affibody protein Zdark1
Keywords keywords	LOV domain, photoreceptor, affibody, optogenetic tool, signaling protein; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.50 Å
Radius of gyration Rg (electron density) rg_electron	19.46 Å
Forward intensity I(0) i0	15733000.00
Molecular weight molecular_weight	28669.0 kDa
Excluded volume excluded_volume	35449 Å³
Envelope volume envelope_volume	42299 Å³
Hydration-shell volume shell_volume	18685 Å³
Envelope diameter envelope_diameter	78.2 Å
Shell Rg shell_rg	25.63 Å
Envelope Rg envelope_rg	20.02 Å
Shape Rg shape_rg	19.40 Å
Total Rg total_rg	20.52 Å
Total atoms total_atoms	2012
Residues n_residues	245
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	74.6 Å
Rg (real space) rg_real	20.54 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	1.5730e+07
I(0) uncertainty (real space) i0_real_error	2.3020e+05
Rg (reciprocal space) rg_reciprocal	20.53 Å
I(0) (reciprocal space) i0_reciprocal	15730000.0000
Solution quality estimate total_estimate	0.7513
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.486
Kurtosis Kurtosis kurtosis	0.070
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3876000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.607; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	NPH1-1
Molecular weight formula_weight	16631.7 kDa
Mutation mutation	C450A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2114

GSLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNARFLQGPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAAEREGVMLIKKTAENIDEAAKEL

来源 Source

来源生物 organism	Avena sativa
通用名 common_name	Oat
NCBI Class编号 ncbi_taxonomy_id	4498
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Z-dark, a small protein based on the Z domain affibody
Molecular weight formula_weight	6565.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C

GSVDNKFNKEKTRAGAEIHSLPNLNVEQKFAFIVSLFDDPSQSANLLAEAKKLNDAQAPK

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI Class编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	94

▼

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5efwb_
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.1 — Bacterial immunoglobulin/albumin-binding domains
Family Family family	a.8.1.1 — Immunoglobulin-binding protein A modules

Domain ID domain_id	d5efwc_
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.1 — Bacterial immunoglobulin/albumin-binding domains
Family Family family	a.8.1.1 — Immunoglobulin-binding protein A modules

CATH v4.4 (3 domains)

Domain ID domain_id	5efwA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

Domain ID domain_id	5efwB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	420 — Immunoglobulin FC, subunit C

Domain ID domain_id	5efwC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	420 — Immunoglobulin FC, subunit C

▶

8. Citations (1)

▶

Unit-cell length a length_a	54.700 Å
Unit-cell length b length_b	54.700 Å
Unit-cell length c length_c	188.030 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	47.280 Å
R factor r_factor	0.2045
R_work r_work	0.2018
R_free r_free	0.2566

fit	/app/data/saxs_computation/ef/5efw/5efw.fit
pddf	/app/data/pr_computation/ef/5efw/5efw.pr.out
profile	/app/data/saxs_computation/ef/5efw/5efw.dat

Crystal structure of LOV2-Zdk1 - the complex of oat LOV2 and the affibody protein Zdark1

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

NPH1-1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)