SAXSdb — 1fk3

▼

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

NONSPECIFIC LIPID-TRANSFER PROTEIN

OrganismNot specified

UniProt P19656

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 28–120	Not recorded	PAM PALMITOLEIC ACID × 1 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；4.5M Na formate, 0.1M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.80 Å R-free 0.236

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 1FK3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AFH LIPID TRANSFER PROTEIN FROM MAIZE SEEDLINGS, NMR, 15 STRUCTURES Deposited 1997-03-07	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–120（93 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；308 K	Resolution not provided
1FK0 STRUCTURAL BASIS OF NON-SPECIFIC LIPID BINDING IN MAIZE LIPID-TRANSFER PROTEIN COMPLEXES WITH CAPRIC ACID REVEALED BY HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHY Deposited 2000-08-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–120（93 aa）	Not recorded	DKA DECANOIC ACID × 1 FMT FORMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；3.3M Na formate, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.80 Å R-free 0.241
1FK1 STRUCTURAL BASIS OF NON-SPECIFIC LIPID BINDING IN MAIZE LIPID-TRANSFER PROTEIN COMPLEXES WITH LAURIC ACID REVEALED BY HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHY Deposited 2000-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–120（93 aa）	Not recorded	DAO LAURIC ACID × 1 FMT FORMIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；4.2M Na formate, 0.2M potassium cyanide, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.80 Å R-free 0.194
1FK2 STRUCTURAL BASIS OF NON-SPECIFIC LIPID BINDING IN MAIZE LIPID-TRANSFER PROTEIN COMPLEXES WITH MYRISTIC ACID REVEALED BY HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHY Deposited 2000-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–120（93 aa）	Not recorded	MYR MYRISTIC ACID × 1 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；4.2M Na formate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.80 Å R-free 0.197
1FK4 STRUCTURAL BASIS OF NON-SPECIFIC LIPID BINDING IN MAIZE LIPID-TRANSFER PROTEIN COMPLEXES WITH STEARIC ACID REVEALED BY HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHY Deposited 2000-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–120（93 aa）	Not recorded	STE STEARIC ACID × 1 FMT FORMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；5.0M Na formate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.80 Å R-free 0.208
1FK5 STRUCTURAL BASIS OF NON-SPECIFIC LIPID BINDING IN MAIZE LIPID-TRANSFER PROTEIN COMPLEXES WITH OLEIC ACID REVEALED BY HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHY Deposited 2000-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–120（93 aa）	Not recorded	OLA OLEIC ACID × 1 FMT FORMIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；3.6-4.8M Na formate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.30 Å R-free 0.188
1FK6 STRUCTURAL BASIS OF NON-SPECIFIC LIPID BINDING IN MAIZE LIPID-TRANSFER PROTEIN COMPLEXES WITH ALPHA-LINOLENIC ACID REVEALED BY HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHY Deposited 2000-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–120（93 aa）	Not recorded	LNL ALPHA-LINOLENIC ACID × 1 FMT FORMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；4.4M Na formate, 0.1M bezene sulfornic acid, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.90 Å R-free 0.274
1FK7 STRUCTURAL BASIS OF NON-SPECIFIC LIPID BINDING IN MAIZE LIPID-TRANSFER PROTEIN COMPLEXES WITH RICINOLEIC ACID REVEALED BY HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHY Deposited 2000-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–120（93 aa）	Not recorded	RCL RICINOLEIC ACID × 1 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；5.0M Na formate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.90 Å R-free 0.274
1MZL MAIZE NONSPECIFIC LIPID TRANSFER PROTEIN Deposited 1995-01-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–120（93 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.219
1MZM MAIZE NONSPECIFIC LIPID TRANSFER PROTEIN COMPLEXED WITH PALMITATE Deposited 1995-01-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–120（93 aa）	Not recorded	PLM PALMITIC ACID × 1 FMT FORMIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.78 Å R-free 0.179

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NLTP_MAIZE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–93； UniProt 28–120

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	1fk3
Deposition date deposition_date	2000-08-09
Structure title title	STRUCTURAL BASIS OF NON-SPECIFIC LIPID BINDING IN MAIZE LIPID-TRANSFER PROTEIN COMPLEXES WITH PALMITOLEIC ACID REVEALED BY HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHY
Keywords keywords	protein-lipid complex, LIPID TRANSPORT; LIPID TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	13.62 Å
Radius of gyration Rg (electron density) rg_electron	12.12 Å
Forward intensity I(0) i0	2206620.00
Molecular weight molecular_weight	9344.0 kDa
Excluded volume excluded_volume	11355 Å³
Envelope volume envelope_volume	12674 Å³
Hydration-shell volume shell_volume	9284 Å³
Envelope diameter envelope_diameter	39.5 Å
Shell Rg shell_rg	17.26 Å
Envelope Rg envelope_rg	12.19 Å
Shape Rg shape_rg	12.14 Å
Total Rg total_rg	13.23 Å
Total atoms total_atoms	646
Residues n_residues	93
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	41.4 Å
Rg (real space) rg_real	13.53 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	2.2070e+06
I(0) uncertainty (real space) i0_real_error	2.4330e+04
Rg (reciprocal space) rg_reciprocal	13.53 Å
I(0) (reciprocal space) i0_reciprocal	2207000.0000
Solution quality estimate total_estimate	0.8204
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.4 Å
Skewness Skewness skewness	0.063
Kurtosis Kurtosis kurtosis	-0.380
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	192600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	NONSPECIFIC LIPID-TRANSFER PROTEIN
Molecular weight formula_weight	9062.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	691

AISCGQVASAIAPCISYARGQGSGPSAGCCSGVRSLNNAARTTADRRAACNCLKNAAAGVSGLNAGNAASIPSKCGVSIPYTISTSTDCSRVN

Entity 2 Entity 2 non-polymer

Description description	PALMITOLEIC ACID
Molecular weight formula_weight	254.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	45

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1fk3a_
Class class	a — All alpha proteins
Fold Fold fold	a.52 — Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
Superfamily Superfamily superfamily	a.52.1 — Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
Family Family family	a.52.1.1 — Plant lipid-transfer and hydrophobic proteins

CATH v4.4 (1 domains)

Domain ID domain_id	1fk3A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	110 — Hydrophobic Seed Protein
Homologous superfamily homologous superfamily	10 — Plant lipid-transfer and hydrophobic proteins

▶

8. Citations (1)

▶

Unit-cell length a length_a	24.790 Å
Unit-cell length b length_b	49.790 Å
Unit-cell length c length_c	69.450 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2000
R_free r_free	0.2360

fit	/app/data/saxs_computation/fk/1fk3/1fk3.fit
pddf	/app/data/pr_computation/fk/1fk3/1fk3.pr.out
profile	/app/data/saxs_computation/fk/1fk3/1fk3.dat

STRUCTURAL BASIS OF NON-SPECIFIC LIPID BINDING IN MAIZE LIPID-TRANSFER PROTEIN COMPLEXES WITH PALMITOLEIC ACID REVEALED BY HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHY

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

NONSPECIFIC LIPID-TRANSFER PROTEIN

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