3qwd

Crystal structure of ClpP from 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 NCTC 8325

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 14	CHLORIDE ION × 7 water × 14	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 7	CHLORIDE ION × 4 water × 7	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 7	CHLORIDE ION × 3 water × 7	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

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	3qwd
Deposition date deposition_date	2011-02-28
Structure title title	Crystal structure of ClpP from Staphylococcus aureus
Keywords keywords	caseinolytic protease, ClpP, serin-protease, Hydrolase; HYDROLASE
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.

3qwd__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3qwd__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3qwd__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	36.41 Å
Rg (electron density)	35.35 Å
Total Rg	35.93 Å
Atom count	9978
Residues	1297
Excluded volume	178610 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3qwd__assembly_1__model_1`	tetradecameric （14）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3qwd__assembly_2__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3qwd__assembly_3__model_1`	heptameric （7）	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 (3)

Entity 1 Entity 1 polymer

Description description	ATP-dependent Clp protease proteolytic subunit
Molecular weight formula_weight	22578.7 kDa
EC 编号 ec_number	3.4.21.92
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N
Atom count atom_count	20404

MNLIPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPETKWSHPQFEK

Source Source

Source organism organism	Staphylococcus aureus subsp. aureus NCTC 8325
NCBI taxonomy ID ncbi_taxonomy_id	93061
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	293

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6. Fold Classification (SCOP + CATH) 31 domains

SCOP 2.08 (17 domains)

Domain ID domain_id	d3qwda_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d3qwdb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d3qwdc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d3qwdc2
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

Domain ID domain_id	d3qwdd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d3qwde_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d3qwdf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d3qwdg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d3qwdh1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d3qwdh2
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

Domain ID domain_id	d3qwdi1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d3qwdi2
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

Domain ID domain_id	d3qwdj_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d3qwdk_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d3qwdl_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d3qwdm_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d3qwdn_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

CATH v4.4 (14 domains)

Domain ID domain_id	3qwdA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3qwdB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3qwdC00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3qwdD00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3qwdE00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3qwdF00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3qwdG00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3qwdH00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3qwdI00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3qwdJ00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3qwdK00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3qwdL00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3qwdM00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3qwdN00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

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Unit-cell length a length_a	172.048 Å
Unit-cell length b length_b	177.974 Å
Unit-cell length c length_c	100.278 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	56

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	88.990 Å
R factor r_factor	0.2086
R_work r_work	0.2076
R_free r_free	0.2261

Crystal structure of ClpP from Staphylococcus aureus

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

ATP-dependent Clp protease proteolytic subunit

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

3qwd__assembly_2__model_1

3qwd__assembly_2__model_1 | I(q)

3qwd__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 31 domains

SCOP 2.08 (17 domains)

CATH v4.4 (14 domains)

7. Citations (1)

Crystal structure of ClpP from Staphylococcus aureus

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

ATP-dependent Clp protease proteolytic subunit

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

3qwd__assembly_2__model_1

3qwd__assembly_2__model_1 | I(q)

3qwd__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 31 domains

SCOP 2.08 (17 domains)

CATH v4.4 (14 domains)

7. Citations (1)