1vyh

PAF-AH Holoenzyme: Lis1/Alfa2

Method: X-RAY DIFFRACTION

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

PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT × 2 （P63005）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT × 2 （P63005）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT × 2 （P63005）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT × 2 （P63005）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT × 2 （P63005）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PA1B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–229； UniProt 1–229 Author chain B； PDBConstruct 1–229； UniProt 1–229 Author chain E； PDBConstruct 1–229； UniProt 1–229 Author chain F； PDBConstruct 1–229； UniProt 1–229 Author chain I； PDBConstruct 1–229； UniProt 1–229 Author chain J； PDBConstruct 1–229； UniProt 1–229 Author chain M； PDBConstruct 1–229； UniProt 1–229 Author chain N； PDBConstruct 1–229； UniProt 1–229 Author chain Q； PDBConstruct 1–229； UniProt 1–229 Author chain R； PDBConstruct 1–229； UniProt 1–229

PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT

MUS MUSCULUS

UniProt P63005

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT × 2 （Q29459）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT × 2 （Q29459）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT × 2 （Q29459）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT × 2 （Q29459）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT × 2 （Q29459）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LIS1_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–410； UniProt 1–409 Author chain D； PDBConstruct 2–410； UniProt 1–409 Author chain G； PDBConstruct 2–410； UniProt 1–409 Author chain H； PDBConstruct 2–410； UniProt 1–409 Author chain K； PDBConstruct 2–410； UniProt 1–409 Author chain L； PDBConstruct 2–410； UniProt 1–409 Author chain O； PDBConstruct 2–410； UniProt 1–409 Author chain P； PDBConstruct 2–410； UniProt 1–409 Author chain S； PDBConstruct 2–410； UniProt 1–409 Author chain T； PDBConstruct 2–410； UniProt 1–409

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	1vyh
Deposition date deposition_date	2004-04-30
Structure title title	PAF-AH Holoenzyme: Lis1/Alfa2
Keywords keywords	;LISSENCEPHALY, ACETYLHYDROLASE, PLATELET ACTIVACTING FACTOR, REGULATOR OF CYTOPLASMIC DYNEIN, HYDROLASE, CELL DIVISION, MITOSIS, NEUROGENESIS, CYTOSKELETON ;; HYDROLASE
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.

1vyh__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1vyh__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vyh__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	34.77 Å
Rg (electron density)	34.31 Å
Total Rg	34.91 Å
Atom count	8318
Residues	1056
Excluded volume	147430 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vyh__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1vyh__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1vyh__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1vyh__assembly_4__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1vyh__assembly_5__model_1`	tetrameric （4）	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)

Entity 1 Entity 1 polymer

Description description	PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
Molecular weight formula_weight	25600.3 kDa
EC 编号 ec_number	3.1.1.47
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,F,I,J,M,N,Q,R
Atom count atom_count	41590

MSQGDSNPAAIPHAAEDIQGDDRWMSQHNRFVLDCKDKEPDVLFVGDSMVQLMQQYEIWRELFSPLHALNFGIGGDTTRHVLWRLKNGELENIKPKVIVVWVGTNNHENTAEEVAGGIEAIVQLINTRQPQAKIIVLGLLPRGEKPNPLRQKNAKVNQLLKVSLPKLANVQLLDTDGGFVHSDGAISCHDMFDFLHLTGGGYAKICKPLHELIMQLLEETPEEKQTTIA

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	PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
Molecular weight formula_weight	46786.1 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,G,H,K,L,O,P,S,T

MVLSQRQRDELNRAIADYLRSNGYEEAYSVFKKEAELDMNEELDKKYAGLLEKKWTSVIRLQKKVMELESKLNEAKEEFTSGGPLGQKRDPKEWIPRPPEKYALSGHRSPVTRVIFHPVFSVMVSASEDATIKVWDYETGDFERTLKGHTDSVQDISFDHSGKLLASCSADMTIKLWDFQGFECIRTMHGHDHNVSSVSIMPNGDHIVSASRDKTIKMWEVQTGYCVKTFTGHREWVRMVRPNQDGTLIASCSNDQTVRVWVVATKECKAELREHRHVVECISWAPESSYSSISEATGSETKKSGKPGPFLLSGSRDKTIKMWDVSTGMCLMTLVGHDNWVRGVLFHSGGKFILSCADDKTLRVWDYKNKRCMKTLNAHEHFVTSLDFHKTAPYVVTGSVDQTVKVWECR

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	SPODOPTERA FRUGIPERDA

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6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

Domain ID domain_id	d1vyha1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.10 — SGNH hydrolase
Family Family family	c.23.10.3 — Acetylhydrolase

Domain ID domain_id	d1vyhb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.10 — SGNH hydrolase
Family Family family	c.23.10.3 — Acetylhydrolase

Domain ID domain_id	d1vyhc1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.4 — WD40 repeat-like
Family Family family	b.69.4.1 — WD40-repeat

Domain ID domain_id	d1vyhd1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.4 — WD40 repeat-like
Family Family family	b.69.4.1 — WD40-repeat

Domain ID domain_id	d1vyhe1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.10 — SGNH hydrolase
Family Family family	c.23.10.3 — Acetylhydrolase

Domain ID domain_id	d1vyhf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.10 — SGNH hydrolase
Family Family family	c.23.10.3 — Acetylhydrolase

Domain ID domain_id	d1vyhg1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.4 — WD40 repeat-like
Family Family family	b.69.4.1 — WD40-repeat

Domain ID domain_id	d1vyhh1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.4 — WD40 repeat-like
Family Family family	b.69.4.1 — WD40-repeat

Domain ID domain_id	d1vyhi1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.10 — SGNH hydrolase
Family Family family	c.23.10.3 — Acetylhydrolase

Domain ID domain_id	d1vyhj1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.10 — SGNH hydrolase
Family Family family	c.23.10.3 — Acetylhydrolase

Domain ID domain_id	d1vyhk1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.4 — WD40 repeat-like
Family Family family	b.69.4.1 — WD40-repeat

Domain ID domain_id	d1vyhl1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.4 — WD40 repeat-like
Family Family family	b.69.4.1 — WD40-repeat

Domain ID domain_id	d1vyhm1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.10 — SGNH hydrolase
Family Family family	c.23.10.3 — Acetylhydrolase

Domain ID domain_id	d1vyhn1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.10 — SGNH hydrolase
Family Family family	c.23.10.3 — Acetylhydrolase

Domain ID domain_id	d1vyho1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.4 — WD40 repeat-like
Family Family family	b.69.4.1 — WD40-repeat

Domain ID domain_id	d1vyhp1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.4 — WD40 repeat-like
Family Family family	b.69.4.1 — WD40-repeat

Domain ID domain_id	d1vyhq1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.10 — SGNH hydrolase
Family Family family	c.23.10.3 — Acetylhydrolase

Domain ID domain_id	d1vyhr1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.10 — SGNH hydrolase
Family Family family	c.23.10.3 — Acetylhydrolase

Domain ID domain_id	d1vyhs1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.4 — WD40 repeat-like
Family Family family	b.69.4.1 — WD40-repeat

Domain ID domain_id	d1vyht1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.4 — WD40 repeat-like
Family Family family	b.69.4.1 — WD40-repeat

CATH v4.4 (20 domains)

Domain ID domain_id	1vyhA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1110 — SGNH hydrolase

Domain ID domain_id	1vyhB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1110 — SGNH hydrolase

Domain ID domain_id	1vyhC01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	1vyhD01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	1vyhE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1110 — SGNH hydrolase

Domain ID domain_id	1vyhF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1110 — SGNH hydrolase

Domain ID domain_id	1vyhG01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	1vyhH01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	1vyhI00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1110 — SGNH hydrolase

Domain ID domain_id	1vyhJ00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1110 — SGNH hydrolase

Domain ID domain_id	1vyhK01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	1vyhL01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	1vyhM00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1110 — SGNH hydrolase

Domain ID domain_id	1vyhN00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1110 — SGNH hydrolase

Domain ID domain_id	1vyhO01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	1vyhP01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	1vyhQ00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1110 — SGNH hydrolase

Domain ID domain_id	1vyhR00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1110 — SGNH hydrolase

Domain ID domain_id	1vyhS01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	1vyhT01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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Unit-cell length a length_a	205.770 Å
Unit-cell length b length_b	101.220 Å
Unit-cell length c length_c	246.130 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.06 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	200.000 Å
R factor r_factor	0.2650
R_work r_work	0.2640
R_free r_free	0.3070

PAF-AH Holoenzyme: Lis1/Alfa2

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

PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT

State in the Current Structure

Other States of the Same Protein in the Database

PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT

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

1vyh__assembly_3__model_1

1vyh__assembly_3__model_1 | I(q)

1vyh__assembly_3__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 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

CATH v4.4 (20 domains)

7. Citations (1)

PAF-AH Holoenzyme: Lis1/Alfa2

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

PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT

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

1vyh__assembly_3__model_1

1vyh__assembly_3__model_1 | I(q)

1vyh__assembly_3__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 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

CATH v4.4 (20 domains)

7. Citations (1)