3v5i

The crystal structure of the mutant ClpP S98A (Staphylococcus aureus)

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

ATP-dependent Clp protease proteolytic subunit

Staphylococcus aureus subsp. aureus

UniProt Q2G036

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 14 water × 14 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 14 water × 14 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name CLPP_STAA8
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–195; UniProt 1–195 Author chain B; PDBConstruct 1–195; UniProt 1–195 Author chain C; PDBConstruct 1–195; UniProt 1–195 Author chain D; PDBConstruct 1–195; UniProt 1–195 Author chain E; PDBConstruct 1–195; UniProt 1–195 Author chain F; PDBConstruct 1–195; UniProt 1–195 Author chain G; PDBConstruct 1–195; UniProt 1–195 Author chain H; PDBConstruct 1–195; UniProt 1–195 Author chain I; PDBConstruct 1–195; UniProt 1–195 Author chain J; PDBConstruct 1–195; UniProt 1–195 Author chain K; PDBConstruct 1–195; UniProt 1–195 Author chain L; PDBConstruct 1–195; UniProt 1–195 Author chain M; PDBConstruct 1–195; UniProt 1–195 Author chain N; PDBConstruct 1–195; UniProt 1–195 Author chain O; PDBConstruct 1–195; UniProt 1–195 Author chain P; PDBConstruct 1–195; UniProt 1–195 Author chain Q; PDBConstruct 1–195; UniProt 1–195 Author chain R; PDBConstruct 1–195; UniProt 1–195 Author chain S; PDBConstruct 1–195; UniProt 1–195 Author chain T; PDBConstruct 1–195; UniProt 1–195 Author chain U; PDBConstruct 1–195; UniProt 1–195 Author chain V; PDBConstruct 1–195; UniProt 1–195 Author chain W; PDBConstruct 1–195; UniProt 1–195 Author chain X; PDBConstruct 1–195; UniProt 1–195 Author chain Y; PDBConstruct 1–195; UniProt 1–195 Author chain Z; PDBConstruct 1–195; UniProt 1–195 Author chain a; PDBConstruct 1–195; UniProt 1–195 Author chain b; PDBConstruct 1–195; UniProt 1–195

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_id3v5i
Deposition date deposition_date2011-12-16
Structure title titleThe crystal structure of the mutant ClpP S98A (Staphylococcus aureus)
Keywords keywordsHydrolase, whole proteome; 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.

3v5i__assembly_1__model_1

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

Download this curve (.dat)

3v5i__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3v5i__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)43.54 Å
Rg (electron density)42.61 Å
Total Rg43.04 Å
Atom count19894
Residues2576
Excluded volume355840 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3v5i__assembly_1__model_1 tetradecameric (14) Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3v5i__assembly_2__model_1 tetradecameric (14) 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)

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6. Fold Classification (SCOP + CATH) 54 domains

SCOP 2.08 (26 domains)

Domain ID domain_idd3v5ia_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5ib_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5ic_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5id_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5ie_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5if_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5ig_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5ih_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5ii_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5ij_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5ik_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5il_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5im_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5in_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5io_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5ip_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5iq_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5ir_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5is_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5it_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5iu_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5iv_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5iw_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5ix_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5iy_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit
Domain ID domain_idd3v5iz_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.14 — ClpP/crotonase
Superfamily Superfamily superfamilyc.14.1 — ClpP/crotonase
Family Family familyc.14.1.1 — Clp protease, ClpP subunit

CATH v4.4 (28 domains)

Domain ID domain_id3v5iA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iB00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iC00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iD00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iE00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iF00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iG00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iH00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iI00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iJ00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iK00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iL00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iM00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iN00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iO00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iP00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iQ00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iR00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iS00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iT00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iU00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iV00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iW00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iX00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iY00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5iZ00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5ia00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Domain ID domain_id3v5ib00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — 2-enoyl-CoA Hydratase; Chain A, domain 1
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7. Citations (1)