5p3u

Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 183

Method: X-RAY DIFFRACTION

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

endothiapepsin

OrganismNot specified

UniProt P11838

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name CARP_CRYPA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–330; UniProt 90–419

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.

2. Structure Basics 2. Structure Basics

Entry ID entry_id5p3u
Deposition date deposition_date2016-06-28
Structure title titleAutomated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 183
Keywords keywordsfragment screening, method development, aspartic protease, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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.

5p3u__assembly_1__model_1

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

Download this curve (.dat)

5p3u__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5p3u__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)20.47 Å
Rg (electron density)19.41 Å
Total Rg20.40 Å
Atom count4585
Residues330
Excluded volume41814 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5p3u__assembly_1__model_1 monomeric (1) Success 4.1.3-1-20251215 (887e7ef) View Download

4. Crystallography and Experiment 4. Crystallography & Experiment

5. Entities and Polymers Entities & Polymers (2)

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5p3ua_
Class classb — All beta proteins
Fold Fold foldb.50 — Acid proteases
Superfamily Superfamily superfamilyb.50.1 — Acid proteases
Family Family familyb.50.1.2 — Pepsin-like

CATH v4.4 (2 domains)

Domain ID domain_id5p3uA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acid Proteases
Domain ID domain_id5p3uA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acid Proteases

7. Citations (1)