SAXSdb — 3wam

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

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

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 8–125	Fragment：UNP RESIDUES 8-125	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.5M di-Ammonium hydrogen citrate, 10% PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.75 Å R-free 0.211
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 8–125	Fragment：UNP RESIDUES 8-125	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.5M di-Ammonium hydrogen citrate, 10% PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.75 Å R-free 0.211

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 3WAM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NCN Solution Structure of the Autophagy-Related Protein LC3C Deposited 2016-04-11	Different construct 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 1–126（126 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；293.15 K；Ionic strength (raw mmCIF value) 171；Pressure 1 NMR sample composition 0.35-0.7 mM [U-15N] Microtubule-associated protein light chain 3C (LC3C), 20 mM PIPES, 150 mM sodium chloride, 0.1 mM EDTA, 2% [U-2H] glycerol, 90% H2O, 10% D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.35-0.7 mM [U-13C; U-15N] Microtubule-associated protein light chain 3C (LC3C), 20 mM PIPES, 150 mM sodium chloride, 0.1 mM EDTA, 2% [U-2H] glycerol, 90% H2O, 10% D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.35-0.7 mM [U-13C; U-15N] Microtubule-associated protein light chain 3C (LC3C), 20 mM PIPES, 150 mM sodium chloride, 0.1 mM EDTA, 2% [U-2H] glycerol, 100% D2O, 100% D2O \| 100% D2O	Resolution not provided
3VVW NDP52 in complex with LC3C Deposited 2012-07-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–126（126 aa） Fragment：UNP residues 1-126	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；16% PEG6000, 0.01M sodium citrate , pH 7.0, Vapor Diffusion, temperature 293K	Resolution 2.50 Å R-free 0.252
3WAP Crystal structure of Atg13 LIR-fused human LC3C_8-125 Deposited 2013-05-06	Different construct 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 8–125（118 aa） Fragment：UNP RESIDUES 436-447, 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；0.1M Sodium acetate trihydrate, 8% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.10 Å R-free 0.273
3WAP Crystal structure of Atg13 LIR-fused human LC3C_8-125 Deposited 2013-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 8–125（118 aa） Fragment：UNP RESIDUES 436-447, 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；0.1M Sodium acetate trihydrate, 8% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.10 Å R-free 0.273
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 8–125（118 aa） Fragment：UNP residues 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 8–125（118 aa） Fragment：UNP residues 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 8–125（118 aa） Fragment：UNP residues 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 8–125（118 aa） Fragment：UNP residues 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 8–125（118 aa） Fragment：UNP residues 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 8–125（118 aa） Fragment：UNP residues 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 8–125（118 aa） Fragment：UNP residues 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 8–125（118 aa） Fragment：UNP residues 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246

4 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MLP3C_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–120； UniProt 8–125

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	3wam
Deposition date deposition_date	2013-05-06
Structure title title	Crystal structure of human LC3C_8-125
Keywords keywords	UBIQUITIN-LIKE FOLD, AUTOPHAGY, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	15.17 Å
Radius of gyration Rg (electron density) rg_electron	13.74 Å
Forward intensity I(0) i0	3528450.00
Molecular weight molecular_weight	13687.0 kDa
Excluded volume excluded_volume	17391 Å³
Envelope volume envelope_volume	19415 Å³
Hydration-shell volume shell_volume	11989 Å³
Envelope diameter envelope_diameter	44.1 Å
Shell Rg shell_rg	19.46 Å
Envelope Rg envelope_rg	14.06 Å
Shape Rg shape_rg	13.73 Å
Total Rg total_rg	15.02 Å
Total atoms total_atoms	963
Residues n_residues	115
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	47.0 Å
Rg (real space) rg_real	15.05 Å
Rg uncertainty (real space) rg_real_error	0.22 Å
I(0) (real space) i0_real	3.5280e+06
I(0) uncertainty (real space) i0_real_error	3.7340e+04
Rg (reciprocal space) rg_reciprocal	15.06 Å
I(0) (reciprocal space) i0_reciprocal	3528000.0000
Solution quality estimate total_estimate	0.8963
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.8 Å
Skewness Skewness skewness	0.090
Kurtosis Kurtosis kurtosis	-0.406
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	751600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.988

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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	Microtubule-associated proteins 1A/1B light chain 3C
Molecular weight formula_weight	13952.2 kDa
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	1077

GSPSVRPFKQRKSLAIRQEEVAGIRAKFPNKIPVVVERYPRETFLPPLDKTKFLVPQELTMTQFLSIIRSRMVLRATEAFYLLVNNKSLVSMSATMAEIYRDYKDEDGFVYMTYASQETF

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	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	114

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3wama_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	3wamA00
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	71.720 Å
Unit-cell length b length_b	71.720 Å
Unit-cell length c length_c	55.650 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	27.830 Å
R factor r_factor	0.1736
R_work r_work	0.1716
R_free r_free	0.2113

fit	/app/data/saxs_computation/wa/3wam/3wam.fit
pddf	/app/data/pr_computation/wa/3wam/3wam.pr.out
profile	/app/data/saxs_computation/wa/3wam/3wam.dat

Crystal structure of human LC3C_8-125

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

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

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