SAXSdb — 2w2o

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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 3	LOW-DENSITY LIPOPROTEIN RECEPTOR × 1 （P01130） CALCIUM ION × 1 water × 3	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, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–299； UniProt 153–451 Author chain P； PDBConstruct 15–114； UniProt 53–152

LOW-DENSITY LIPOPROTEIN RECEPTOR

HOMO SAPIENS

UniProt P01130

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9 × 1 （Q8NBP7） PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9 × 1 （Q8NBP7） CALCIUM ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LDLR_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 28–107； UniProt 314–393

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	2w2o
Deposition date deposition_date	2008-11-03
Structure title title	PCSK9-deltaC D374Y mutant bound to WT EGF-A of LDLR
Keywords keywords	;HYDROLASE-RECEPTOR COMPLEX, PCSK9, LDLR, PROPROTEIN CONVERTASE, LOW-DENSITY LIPOPROTEIN RECEPTOR, EGF, CARDIOVASCULAR DISEASE, FAMILIAL HYPERCHOLESTEROLEMIA, LIPID METABOLISM, SERINE PROTEASE, HYDROLASE, LIPID TRANSPORT, STEROID METABOLISM, RECEPTOR ;; HYDROLASE/RECEPTOR
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.

2w2o__assembly_1__model_1

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

Download this curve (.dat)

2w2o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2w2o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.61 Å
Rg (electron density)	22.78 Å
Total Rg	23.65 Å
Atom count	3126
Residues	413
Excluded volume	55547 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2w2o__assembly_1__model_1`	trimeric （3）	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	33156.3 kDa
EC 编号 ec_number	3.4.21.-
Mutation mutation	YES
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	3155

SIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSYCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHGAAGTAAASHHHHHH

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	LOW-DENSITY LIPOPROTEIN RECEPTOR
Molecular weight formula_weight	12095.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MKHHHHHHPMSDYDIPTTENLYFQGAMGTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACK

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	PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
Molecular weight formula_weight	12679.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

MKGSKGSKGSKPMSAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ

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	CALCIUM ION
Molecular weight formula_weight	40.1 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	19

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2w2oa_
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	d2w2oe1
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.0 — automated matches

Domain ID domain_id	d2w2oe2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	2w2oA00
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	2w2oE00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	2w2oP01
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

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Unit-cell length a length_a	85.948 Å
Unit-cell length b length_b	85.948 Å
Unit-cell length c length_c	218.329 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.620 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2284
R_work r_work	0.2266
R_free r_free	0.2631

PCSK9-deltaC D374Y mutant bound to WT EGF-A of LDLR

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

LOW-DENSITY LIPOPROTEIN RECEPTOR

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

2w2o__assembly_1__model_1

2w2o__assembly_1__model_1 | I(q)

2w2o__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

PCSK9-deltaC D374Y mutant bound to WT EGF-A of LDLR

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

LOW-DENSITY LIPOPROTEIN RECEPTOR

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

2w2o__assembly_1__model_1

2w2o__assembly_1__model_1 | I(q)

2w2o__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)