5dpw

Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125

Method: X-RAY DIFFRACTION

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Pleckstrin homology domain-containing family M member 1 × 1 （Q9Y4G2） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Pleckstrin homology domain-containing family M member 1 × 1 （Q9Y4G2） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Pleckstrin homology domain-containing family M member 1 × 1 （Q9Y4G2） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Pleckstrin homology domain-containing family M member 1 × 1 （Q9Y4G2） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Pleckstrin homology domain-containing family M member 1 × 1 （Q9Y4G2） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Pleckstrin homology domain-containing family M member 1 × 1 （Q9Y4G2） water × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Pleckstrin homology domain-containing family M member 1 × 1 （Q9Y4G2） water × 1	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	Pleckstrin homology domain-containing family M member 1 × 1 （Q9Y4G2） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MLP3C_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–118； UniProt 8–125 Author chain C； PDBConstruct 1–118； UniProt 8–125 Author chain E； PDBConstruct 1–118； UniProt 8–125 Author chain G； PDBConstruct 1–118； UniProt 8–125 Author chain I； PDBConstruct 1–118； UniProt 8–125 Author chain K； PDBConstruct 1–118； UniProt 8–125 Author chain M； PDBConstruct 1–118； UniProt 8–125 Author chain O； PDBConstruct 1–118； UniProt 8–125

Pleckstrin homology domain-containing family M member 1

Homo sapiens

UniProt Q9Y4G2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Microtubule-associated proteins 1A/1B light chain 3C × 1 （Q9BXW4） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Microtubule-associated proteins 1A/1B light chain 3C × 1 （Q9BXW4） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Microtubule-associated proteins 1A/1B light chain 3C × 1 （Q9BXW4） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Microtubule-associated proteins 1A/1B light chain 3C × 1 （Q9BXW4） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Microtubule-associated proteins 1A/1B light chain 3C × 1 （Q9BXW4） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Microtubule-associated proteins 1A/1B light chain 3C × 1 （Q9BXW4） water × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Microtubule-associated proteins 1A/1B light chain 3C × 1 （Q9BXW4） water × 1	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	Microtubule-associated proteins 1A/1B light chain 3C × 1 （Q9BXW4） water × 2	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–14； UniProt 629–642 Author chain D； PDBConstruct 1–14； UniProt 629–642 Author chain F； PDBConstruct 1–14； UniProt 629–642 Author chain H； PDBConstruct 1–14； UniProt 629–642 Author chain J； PDBConstruct 1–14； UniProt 629–642 Author chain L； PDBConstruct 1–14； UniProt 629–642 Author chain N； PDBConstruct 1–14； UniProt 629–642 Author chain P； PDBConstruct 1–14； UniProt 629–642

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	5dpw
Deposition date deposition_date	2015-09-14
Structure title title	Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125
Keywords keywords	Autophagy, 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.

5dpw__assembly_1__model_1

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

Download this curve (.dat)

5dpw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5dpw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.57 Å
Rg (electron density)	14.15 Å
Total Rg	15.41 Å
Atom count	2073
Residues	124
Excluded volume	18606 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dpw__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5dpw__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5dpw__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5dpw__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5dpw__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`5dpw__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`5dpw__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`5dpw__assembly_8__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	Microtubule-associated proteins 1A/1B light chain 3C
Molecular weight formula_weight	13808.1 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O
Atom count atom_count	16830

PSVRPFKQRKSLAIRQEEVAGIRAKFPNKIPVVVERYPRETFLPPLDKTKFLVPQELTMTQFLSIIRSRMVLRATEAFYLLVNNKSLVSMSATMAEIYRDYKDEDGFVYMTYASQETF

Source Source

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

Entity 2 Entity 2 polymer

Description description	Pleckstrin homology domain-containing family M member 1
Molecular weight formula_weight	1746.8 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L,N,P

PQQEDEWVNVQYPD

Source Source

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	160

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5dpwa_
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	d5dpwc_
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	d5dpwe_
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	d5dpwg_
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	d5dpwi_
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	d5dpwk_
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	d5dpwm_
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	d5dpwo_
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 (8 domains)

Domain ID domain_id	5dpwA00
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	5dpwC00
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	5dpwE00
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	5dpwG00
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	5dpwI00
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	5dpwK00
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	5dpwM00
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	5dpwO00
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	54.140 Å
Unit-cell length b length_b	73.225 Å
Unit-cell length c length_c	89.048 Å
Unit-cell angle α angle_alpha	89.96 °
Unit-cell angle β angle_beta	89.99 °
Unit-cell angle γ angle_gamma	77.31 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.185 Å
Low-resolution limit resolution_low	38.610 Å
R factor r_factor	0.2006
R_work r_work	0.1996
R_free r_free	0.2457

Crystal structure of PLEKHM1 LIR in complex with 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

Pleckstrin homology domain-containing family M member 1

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

5dpw__assembly_1__model_1

5dpw__assembly_1__model_1 | I(q)

5dpw__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of PLEKHM1 LIR in complex with 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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Pleckstrin homology domain-containing family M member 1

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

5dpw__assembly_1__model_1

5dpw__assembly_1__model_1 | I(q)

5dpw__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)