SAXSdb — 5wrd

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

Microtubule-associated proteins 1A/1B light chain 3B

Mus musculus

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 1–125	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate, 0.1M sodium citrate tribasic dihydrate (pH 5.6), 0.2M potassium sodium tartrate tetrahydrate	Resolution 1.90 Å R-free 0.244
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–125	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate, 0.1M sodium citrate tribasic dihydrate (pH 5.6), 0.2M potassium sodium tartrate tetrahydrate	Resolution 1.90 Å R-free 0.244
5	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–125	Not recorded	Peptide from FYVE and coiled-coil domain-containing protein 1 × 1 （Q8VDC1） GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate, 0.1M sodium citrate tribasic dihydrate (pH 5.6), 0.2M potassium sodium tartrate tetrahydrate	Resolution 1.90 Å R-free 0.244
6	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–125	Not recorded	Peptide from FYVE and coiled-coil domain-containing protein 1 × 1 （Q8VDC1） GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate, 0.1M sodium citrate tribasic dihydrate (pH 5.6), 0.2M potassium sodium tartrate tetrahydrate	Resolution 1.90 Å R-free 0.244

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 5WRD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5YIQ Crystal structure of AnkG LIR/LC3B complex Deposited 2017-10-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–125（125 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；289 K；10% v/v 2-propanol, 0.2 M zinc acetate, 0.1 M MES buffer (pH 6.5)	Resolution 2.60 Å R-free 0.259
5YIS Crystal Structure of AnkB LIR/LC3B complex Deposited 2017-10-06	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–125（125 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；289 K；2.4 M ammonium phosphate dibasic, 0.1 M Tris buffer (pH 8.5)	Resolution 2.20 Å R-free 0.250
5YIS Crystal Structure of AnkB LIR/LC3B complex Deposited 2017-10-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–125（125 aa）	Not recorded	GOL GLYCEROL × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；289 K；2.4 M ammonium phosphate dibasic, 0.1 M Tris buffer (pH 8.5)	Resolution 2.20 Å R-free 0.250

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

View Construct and Data Evidence

UniProt name	MLP3B_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–125； UniProt 1–125 Author chain B； PDBConstruct 1–125； UniProt 1–125

Peptide from FYVE and coiled-coil domain-containing protein 1

OrganismNot specified

UniProt Q8VDC1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1235–1253	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate, 0.1M sodium citrate tribasic dihydrate (pH 5.6), 0.2M potassium sodium tartrate tetrahydrate	Resolution 1.90 Å R-free 0.244
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1235–1253	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate, 0.1M sodium citrate tribasic dihydrate (pH 5.6), 0.2M potassium sodium tartrate tetrahydrate	Resolution 1.90 Å R-free 0.244
5	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1235–1253	Not recorded	Microtubule-associated proteins 1A/1B light chain 3B × 1 （Q9CQV6） GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate, 0.1M sodium citrate tribasic dihydrate (pH 5.6), 0.2M potassium sodium tartrate tetrahydrate	Resolution 1.90 Å R-free 0.244
6	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1235–1253	Not recorded	Microtubule-associated proteins 1A/1B light chain 3B × 1 （Q9CQV6） GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate, 0.1M sodium citrate tribasic dihydrate (pH 5.6), 0.2M potassium sodium tartrate tetrahydrate	Resolution 1.90 Å R-free 0.244

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	FYCO1_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–19； UniProt 1235–1253 Author chain D； PDBConstruct 1–19； UniProt 1235–1253

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	5wrd
Deposition date deposition_date	2016-12-01
Structure title title	Crystal structure of LC3B in complex with FYCO1 LIR
Keywords keywords	Autophagy, PROTEIN BINDING; PROTEIN BINDING
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	22.27 Å
Radius of gyration Rg (electron density) rg_electron	21.21 Å
Forward intensity I(0) i0	17953900.00
Molecular weight molecular_weight	32161.0 kDa
Excluded volume excluded_volume	40330 Å³
Envelope volume envelope_volume	47782 Å³
Hydration-shell volume shell_volume	19609 Å³
Envelope diameter envelope_diameter	71.8 Å
Shell Rg shell_rg	26.85 Å
Envelope Rg envelope_rg	21.31 Å
Shape Rg shape_rg	21.20 Å
Total Rg total_rg	22.01 Å
Total atoms total_atoms	2264
Residues n_residues	272
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	70.8 Å
Rg (real space) rg_real	22.29 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	1.7950e+07
I(0) uncertainty (real space) i0_real_error	1.8290e+05
Rg (reciprocal space) rg_reciprocal	22.29 Å
I(0) (reciprocal space) i0_reciprocal	17950000.0000
Solution quality estimate total_estimate	0.8968
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.6 Å
Skewness Skewness skewness	0.382
Kurtosis Kurtosis kurtosis	-0.434
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4438000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.986

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Microtubule-associated proteins 1A/1B light chain 3B
Molecular weight formula_weight	14637.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2314

MPSEKTFKQRRSFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYESERDEDGFLYMVYASQETFGTAMAV

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Peptide from FYVE and coiled-coil domain-containing protein 1
Molecular weight formula_weight	2183.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

DDAVFDIITDEELCQIQES

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	50

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5wrdA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	5wrdB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	113.412 Å
Unit-cell length b length_b	44.613 Å
Unit-cell length c length_c	63.582 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	120.29 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1909
R_work r_work	0.1881
R_free r_free	0.2442

fit	/app/data/saxs_computation/wr/5wrd/5wrd.fit
pddf	/app/data/pr_computation/wr/5wrd/5wrd.pr.out
profile	/app/data/saxs_computation/wr/5wrd/5wrd.dat

Crystal structure of LC3B in complex with FYCO1 LIR

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

Microtubule-associated proteins 1A/1B light chain 3B

State in the Current Structure

Other States of the Same Protein in the Database

Peptide from FYVE and coiled-coil domain-containing protein 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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)