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5oca

PCSK9:Fab Complex with Dextran Sulfate

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Proprotein convertase subtilisin/kexin type 9

Homo sapiens

UniProt Q8NBP7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 4 其他Polymer 1 Fab from LDLR competitive antibody: Heavy chain × 1 Fab from LDLR competitive antibody: Light chain × 1 2,3,4-tri-O-sulfo-beta-D-altropyranose-(1-6)-2,3-di-O-sulfo-alpha-L-glucopyranose × 1 SODIUM ION × 2 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2p4e 2p4e 6u26 6u26

4 assemblies

Homodimer
2p4e 2qtw 4k8r 6u2n 6u2p 6u3x 8wfr 9hz3 9szy

9 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
10sb 2w2m 2w2n 2w2o 2w2p 2w2q 2xtj 3bps 3gcw 3gcx 3h42 3m0c

56 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name PCSK9_HUMAN
Isoform —
PDB entities 1, 2
Chains and sequence ranges Author chain A； PDBConstruct 5–126； UniProt 31–152 Author chain B； PDBConstruct 1–540； UniProt 153–692

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_id5oca
Deposition date deposition_date2017-06-30
Structure title titlePCSK9:Fab Complex with Dextran Sulfate
Keywords keywords;HYDROLASE, PROTEIN FAB COMPLEX, AUTOCATALYTIC CLEAVAGE, CHOLESTEROL METABOLISM, DISEASE MUTATION, DISULFIDE BOND, GLYCOPROTEIN, LIPID METABOLISM, PHOSPHOPROTEIN, PROTEASE, SECRETED, SERINE PROTEASE, STEROID METABOLISM, ZYMOGEN, HYDROLASE-IMMUNE SYSTEM COMPLEX ;; HYDROLASE
Experimental Method methodX-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.

5oca__assembly_1__model_1

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

Download this curve (.dat)

5oca__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5oca__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）36.85 Å
Rg (electron density)36.86 Å
Total Rg37.28 Å
Atom count7657
Residues1020
Excluded volume135100 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5oca__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 (7)

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd5ocab1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.41 — Subtilisin-like
Superfamily Superfamily superfamilyc.41.1 — Subtilisin-like
Family Family familyc.41.1.1 — Subtilases
Domain ID domain_idd5ocab2
Class classg — Small proteins
Fold Fold foldg.77 — Resistin
Superfamily Superfamily superfamilyg.77.1 — Resistin
Family Family familyg.77.1.2 — PCSK9 C-terminal domain-like
Domain ID domain_idd5ocah_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd5ocal1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd5ocal2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (5 domains)

Domain ID domain_id5ocaA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily80 — Peptidase S8 propeptide/proteinase inhibitor I9
Domain ID domain_id5ocaB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily200 — Peptidase S8/S53 domain
Domain ID domain_id5ocaB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily690 — Proprotein convertase subtilisin/kexin type 9
Domain ID domain_id5ocaH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5ocaL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (1)