6n80

S. aureus ClpP bound to anti-4a

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 (strain 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	N-[(1R)-1-borono-3-methylbutyl]-N~2~-(2-chloro-4-methoxybenzene-1-carbonyl)-L-leucinamide × 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 I； 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 S； PDBConstruct 1–195； UniProt 1–195 Author chain T； 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	6n80
Deposition date deposition_date	2018-11-28
Structure title title	S. aureus ClpP bound to anti-4a
Keywords keywords	ClpP, 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.

6n80__assembly_1__model_1

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

Download this curve (.dat)

6n80__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6n80__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.17 Å
Rg (electron density)	42.23 Å
Total Rg	42.60 Å
Atom count	19435
Residues	2524
Excluded volume	347250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6n80__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	ATP-dependent Clp protease proteolytic subunit
Molecular weight formula_weight	22607.7 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,I,K,L,M,N,S,T
Atom count atom_count	21063

MNLIPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPETKLEHHHHHH

Source Source

Source organism organism	Staphylococcus aureus (strain NCTC 8325)
NCBI taxonomy ID ncbi_taxonomy_id	93061
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	N-[(1R)-1-borono-3-methylbutyl]-N~2~-(2-chloro-4-methoxybenzene-1-carbonyl)-L-leucinamide
Molecular weight formula_weight	412.7 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1579

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d6n80a_
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	d6n80b_
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	d6n80c_
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	d6n80d_
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	d6n80e_
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	d6n80f_
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	d6n80g_
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	d6n80i_
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	d6n80k_
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	d6n80l_
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	d6n80m_
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	d6n80n_
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	d6n80s_
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	d6n80t_
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	6n80A00
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	6n80B00
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	6n80C00
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	6n80D00
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	6n80E00
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	6n80F00
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	6n80G00
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	6n80I00
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	6n80K00
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	6n80L00
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	6n80M00
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	6n80N00
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	6n80S00
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	6n80T00
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	94.332 Å
Unit-cell length b length_b	126.115 Å
Unit-cell length c length_c	145.461 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	28

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.960 Å
Low-resolution limit resolution_low	43.241 Å
R factor r_factor	0.1726
R_work r_work	0.1712
R_free r_free	0.2006

S. aureus ClpP bound to anti-4a

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

6n80__assembly_1__model_1

6n80__assembly_1__model_1 | I(q)

6n80__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 (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) 28 domains

SCOP 2.08 (14 domains)

CATH v4.4 (14 domains)

7. Citations (1)

S. aureus ClpP bound to anti-4a

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

6n80__assembly_1__model_1

6n80__assembly_1__model_1 | I(q)

6n80__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 (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) 28 domains

SCOP 2.08 (14 domains)

CATH v4.4 (14 domains)

7. Citations (1)