SAXSdb — 6u38

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

Proprotein convertase subtilisin/kexin type 9

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	Fab Heavy Chain × 1 Fab Light Chain × 1 ;2-fluoro-4-{[(1R)-1-methyl-6-{[(2S)-oxan-2-yl]methoxy}-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}benzoic acid ; × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCSK9_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–662； UniProt 31–692 Author chain B； PDBConstruct 1–662； UniProt 31–692

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	6u38
Deposition date deposition_date	2019-08-21
Structure title title	PCSK9 in complex with a Fab and compound 8
Keywords keywords	Serine Type Endopeptidase Activity Proteolysis, HYDROLASE, HYDROLASE-Immune System complex; HYDROLASE/Immune System
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.

6u38__assembly_1__model_1

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

Download this curve (.dat)

6u38__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6u38__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.29 Å
Rg (electron density)	41.51 Å
Total Rg	41.59 Å
Atom count	7415
Residues	1000
Excluded volume	130810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6u38__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	Proprotein convertase subtilisin/kexin type 9
Molecular weight formula_weight	76081.7 kDa
EC 编号 ec_number	3.4.21.-
Mutation mutation	V474I, G670E
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	7473

QEDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQSIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHGAGWQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLGTHKPPVLRPRGQPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTLTGCSALPGTSHVLGAYAVDNTCVVRSRDVSTTGSTSEEAVTAVAICCRSRHLAQASQELQKGNSADIQHSGGRSSLEGPRFEGKPIPNPLLGLDSTRTGHHHHHH

Source Source

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

Entity 2 Entity 2 polymer

Description description	Fab Heavy Chain
Molecular weight formula_weight	26546.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQLLESGGGLVQPGGSLRLSCKASGYTFSSYGMYWVRQAPGKGLEWIGWIDPGSGGTKYNEKFKGKATISRDNSKNTLYLQMNSLRAEDTAVYYCARERYGYYFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTAAAYPYDVPDYAGGHHHHHH

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 polymer

Description description	Fab Light Chain
Molecular weight formula_weight	23437.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

EIVLTQSPATLSLSPGERATITCRASQYVGSYLNWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQVWDSSPPVVFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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 4 Entity 4 non-polymer

Description description	;2-fluoro-4-{[(1R)-1-methyl-6-{[(2S)-oxan-2-yl]methoxy}-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}benzoic acid ;
Molecular weight formula_weight	555.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	58

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6u38b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.41 — Subtilisin-like
Superfamily Superfamily superfamily	c.41.1 — Subtilisin-like
Family Family family	c.41.1.1 — Subtilases

Domain ID domain_id	d6u38b2
Class class	g — Small proteins
Fold Fold fold	g.77 — Resistin
Superfamily Superfamily superfamily	g.77.1 — Resistin
Family Family family	g.77.1.2 — PCSK9 C-terminal domain-like

Domain ID domain_id	d6u38l1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6u38l2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (5 domains)

Domain ID domain_id	6u38A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	80 — Peptidase S8 propeptide/proteinase inhibitor I9

Domain ID domain_id	6u38B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	200 — Peptidase S8/S53 domain

Domain ID domain_id	6u38B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	690 — Proprotein convertase subtilisin/kexin type 9

Domain ID domain_id	6u38H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6u38L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	155.033 Å
Unit-cell length b length_b	155.033 Å
Unit-cell length c length_c	151.919 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	12

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.730 Å
Low-resolution limit resolution_low	38.760 Å
R factor r_factor	0.2280
R_work r_work	0.2270
R_free r_free	0.2430

PCSK9 in complex with a Fab and compound 8

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

Proprotein convertase subtilisin/kexin type 9

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

6u38__assembly_1__model_1

6u38__assembly_1__model_1 | I(q)

6u38__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (4 domains)

CATH v4.4 (5 domains)

7. Citations (1)

PCSK9 in complex with a Fab and compound 8

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

Proprotein convertase subtilisin/kexin type 9

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

6u38__assembly_1__model_1

6u38__assembly_1__model_1 | I(q)

6u38__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (4 domains)

CATH v4.4 (5 domains)

7. Citations (1)