SAXSdb — 3eyc

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

Lipocalin-1

Homo sapiens

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 23–176	Fragment：residues 5-166 Mutation：C101S, D158A	BU1 1,4-BUTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；27% PEG3350, 0.8% 1.4-Butanediol, 200mM NaCl, 100mM Tris/HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.274
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 23–176	Fragment：residues 5-166 Mutation：C101S, D158A	BU1 1,4-BUTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；27% PEG3350, 0.8% 1.4-Butanediol, 200mM NaCl, 100mM Tris/HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.274
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 23–176	Fragment：residues 5-166 Mutation：C101S, D158A	BU1 1,4-BUTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；27% PEG3350, 0.8% 1.4-Butanediol, 200mM NaCl, 100mM Tris/HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.274
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 23–176	Fragment：residues 5-166 Mutation：C101S, D158A	BU1 1,4-BUTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；27% PEG3350, 0.8% 1.4-Butanediol, 200mM NaCl, 100mM Tris/HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.274

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 3EYC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1XKI Crystal structure of human tear lipocalin/von Ebners gland protein Deposited 2004-09-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–176（154 aa）	Mutation：C101S, D158A	ZN ZINC ION × 3 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；285 K；Tris/HCl, Zn-acetate, ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.80 Å R-free 0.254
4QAF Crystal structure of an engineered lipocalin (Anticalin) in complex with VEGF(8-109) Deposited 2014-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 23–174（152 aa） Fragment：UNP residues 23-174 Chain B 23–174（152 aa） Fragment：UNP residues 23-174	Mutation：;R26V,E27G,F28A,P29L,E30R,M31C,N32L,L33A,E34G,T37I,M39T,L56H,S58K,C61S,E69S,K76I,D80I,K83I,Y87K,I89G,C101S,E104C,H106S,K108V,R111P,K114W,C153S ; Mutation：;R26V,E27G,F28A,P29L,E30R,M31C,N32L,L33A,E34G,T37I,M39T,L56H,S58K,C61S,E69S,K76I,D80I,K83I,Y87K,I89G,C101S,E104C,H106S,K108V,R111P,K114W,C153S ;	OMA 10-{(1R,2R)-2-[(2E)-hex-2-en-1-yl]cyclopropyl}decanoic acid × 2 SO4 SULFATE ION × 3 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；293 K；1 M sodium chloride, 0.2 M lithium sulfate, 7.5% w/v dextran sulfate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.242
5T43 NMR Structure of Apo-form Human Tear Lipocalin Deposited 2016-08-28	Different construct Different mutation/modification 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 19–176（158 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；310 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] Lipocalin, 90 % H2O, 10 % D2O, 50 mM sodium phosphate, 0.04 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LCN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–154； UniProt 23–176 Author chain B； PDBConstruct 1–154； UniProt 23–176 Author chain C； PDBConstruct 1–154； UniProt 23–176 Author chain D； PDBConstruct 1–154； UniProt 23–176

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	3eyc
Deposition date deposition_date	2008-10-20
Structure title title	New crystal structure of human tear lipocalin in complex with 1,4-butanediol in space group P21
Keywords keywords	transport protein, ligand-binding protein, beta-barrel, Secreted, Sensory transduction, Taste, Transport; TRANSPORT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	31.55 Å
Radius of gyration Rg (electron density) rg_electron	31.09 Å
Forward intensity I(0) i0	63547200.00
Molecular weight molecular_weight	61873.0 kDa
Excluded volume excluded_volume	77377 Å³
Envelope volume envelope_volume	108130 Å³
Hydration-shell volume shell_volume	31007 Å³
Envelope diameter envelope_diameter	106.8 Å
Shell Rg shell_rg	35.77 Å
Envelope Rg envelope_rg	30.47 Å
Shape Rg shape_rg	31.10 Å
Total Rg total_rg	31.51 Å
Total atoms total_atoms	4339
Residues n_residues	557
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

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

Maximum dimension Dmax dmax	99.3 Å
Rg (real space) rg_real	31.56 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	6.3550e+07
I(0) uncertainty (real space) i0_real_error	1.0190e+06
Rg (reciprocal space) rg_reciprocal	31.56 Å
I(0) (reciprocal space) i0_reciprocal	63550000.0000
Solution quality estimate total_estimate	0.8944
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	27.8 Å
Skewness Skewness skewness	0.235
Kurtosis Kurtosis kurtosis	-0.648
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21720000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.861

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Lipocalin-1
Molecular weight formula_weight	17949.2 kDa
Mutation mutation	C101S, D158A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4524

ASDEEIQDVSGTWYLKAMTVDREFPEMNLESVTPMTLTTLEGGNLEAKVTMLISGRCQEVKAVLEKTDEPGKYTADGGKHVAYIIRSHVKDHYIFYSEGELHGKPVRGVKLVGRDPKNNLEALEDFEKAAGARGLSTESILIPRQSETCSPGSAWSHPQFEK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,4-BUTANEDIOL
Molecular weight formula_weight	90.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	185

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3eyca_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.1 — Retinol binding protein-like

Domain ID domain_id	d3eycb_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.1 — Retinol binding protein-like

Domain ID domain_id	d3eycc_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.1 — Retinol binding protein-like

Domain ID domain_id	d3eycd_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.1 — Retinol binding protein-like

CATH v4.4 (4 domains)

Domain ID domain_id	3eycA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

Domain ID domain_id	3eycB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

Domain ID domain_id	3eycC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

Domain ID domain_id	3eycD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

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8. Citations (1)

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Unit-cell length a length_a	63.907 Å
Unit-cell length b length_b	34.166 Å
Unit-cell length c length_c	143.481 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.35 °
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	2.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2280
R_free r_free	0.2740

fit	/app/data/saxs_computation/ey/3eyc/3eyc.fit
pddf	/app/data/pr_computation/ey/3eyc/3eyc.pr.out
profile	/app/data/saxs_computation/ey/3eyc/3eyc.dat

New crystal structure of human tear lipocalin in complex with 1,4-butanediol in space group P21

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

Lipocalin-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