SAXSdb — 5dpr

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

Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count
3	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count
4	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MLP3A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 17–136； UniProt 2–121 Author chain B； PDBConstruct 17–136； UniProt 2–121 Author chain C； PDBConstruct 17–136； UniProt 2–121 Author chain D； PDBConstruct 17–136； UniProt 2–121

Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A

Homo sapiens

UniProt Q9Y4G2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count
3	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count
4	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PKHM1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–14； UniProt 627–638 Author chain B； PDBConstruct 3–14； UniProt 627–638 Author chain C； PDBConstruct 3–14； UniProt 627–638 Author chain D； PDBConstruct 3–14； UniProt 627–638

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	5dpr
Deposition date deposition_date	2015-09-14
Structure title title	Crystal structure of PLEKHM1 LIR-fused human LC3A_2-121
Keywords keywords	Autophagy; PLEKHM1; Atg8; LC3; GABARAP, chimeric protein, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5dpr__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5dpr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5dpr__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	16.56 Å
Rg (electron density)	15.29 Å
Total Rg	16.33 Å
Atom count	1973
Residues	124
Excluded volume	17763 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dpr__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5dpr__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5dpr__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5dpr__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (2)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5dpra_
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.15.1.3 — GABARAP-like

Domain ID domain_id	d5dprb_
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.15.1.3 — GABARAP-like

Domain ID domain_id	d5dprc_
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.15.1.3 — GABARAP-like

Domain ID domain_id	d5dprd_
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.15.1.3 — GABARAP-like

CATH v4.4 (4 domains)

Domain ID domain_id	5dprA00
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	5dprB00
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	5dprC00
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	5dprD00
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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Unit-cell length a length_a	62.700 Å
Unit-cell length b length_b	63.082 Å
Unit-cell length c length_c	84.924 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.94 °
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	2.500 Å
Low-resolution limit resolution_low	45.567 Å
R factor r_factor	0.2202
R_work r_work	0.2179
R_free r_free	0.2608

Description description	Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A
Molecular weight formula_weight	15932.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8157

Crystal structure of PLEKHM1 LIR-fused human LC3A_2-121

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

Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A

State in the Current Structure

Other States of the Same Protein in the Database

Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5dpr__assembly_1__model_1

5dpr__assembly_1__model_1 | I(q)

5dpr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	42

Crystal structure of PLEKHM1 LIR-fused human LC3A_2-121

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

Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5dpr__assembly_1__model_1

5dpr__assembly_1__model_1 | I(q)

5dpr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)