SAXSdb — 6pbs

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

ATP-dependent Clp protease ATP-binding subunit ClpC1

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	ecumicin × 2 ACETATE ION × 2 water × 3	Consistent with protein count
10	Protein heterocomplex	Heteromer	Protein 3	ecumicin × 2 ACETATE ION × 1 water × 3	Consistent with protein count
11	Protein heterocomplex	Heteromer	Protein 3	ecumicin × 2 ACETATE ION × 1 water × 3	Consistent with protein count
12	Protein heterocomplex	Heteromer	Protein 3	ecumicin × 2 ACETATE ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	ecumicin × 2 ACETATE ION × 2 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	ecumicin × 2 ACETATE ION × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	ecumicin × 2 ACETATE ION × 4 water × 3	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 3	ecumicin × 2 ACETATE ION × 3 water × 3	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 3	ecumicin × 2 ACETATE ION × 2 water × 3	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 3	ecumicin × 2 ACETATE ION × 1 water × 3	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 3	ecumicin × 2 ACETATE ION × 1 water × 3	Consistent with protein count
9	Protein heterocomplex	Heteromer	Protein 3	ecumicin × 2 ACETATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CLPC1_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–145； UniProt 1–145 Author chain B； PDBConstruct 1–145； UniProt 1–145 Author chain C； PDBConstruct 1–145； UniProt 1–145 Author chain G； PDBConstruct 1–145； UniProt 1–145 Author chain I； PDBConstruct 1–145； UniProt 1–145 Author chain K； PDBConstruct 1–145； UniProt 1–145 Author chain M； PDBConstruct 1–145； UniProt 1–145 Author chain O； PDBConstruct 1–145； UniProt 1–145 Author chain T； PDBConstruct 1–145； UniProt 1–145 Author chain W； PDBConstruct 1–145； UniProt 1–145 Author chain Y； PDBConstruct 1–145； UniProt 1–145 Author chain e； PDBConstruct 1–145； UniProt 1–145

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	6pbs
Deposition date deposition_date	2019-06-14
Structure title title	Structure of ClpC1-NTD in complex with Ecumicin
Keywords keywords	ClpC1-NTD, Ecumicin, ATPase, Mycobacterium tuberculosis, CHAPERONE-ANTIBIOTIC complex; CHAPERONE/ANTIBIOTIC
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.

6pbs__assembly_1__model_1

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

Download this curve (.dat)

6pbs__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6pbs__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.59 Å
Rg (electron density)	15.37 Å
Total Rg	16.64 Å
Atom count	1349
Residues	156
Excluded volume	24608 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6pbs__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6pbs__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6pbs__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6pbs__assembly_4__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6pbs__assembly_5__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`6pbs__assembly_6__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`6pbs__assembly_7__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`6pbs__assembly_8__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`6pbs__assembly_9__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`6pbs__assembly_10__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`6pbs__assembly_11__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`6pbs__assembly_12__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	ATP-dependent Clp protease ATP-binding subunit ClpC1
Molecular weight formula_weight	17529.1 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,I,C,W,Y,e,B,G,K,M,O,T
Atom count atom_count	16993

MFERFTDRARRVVVLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKSLESLGISLEGVRSQVEEIIGQGQQAPSGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVAAQVLVKLGAELTRVRQQVIQLLSGYKLAAALEHHHHHH

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	ecumicin
Molecular weight formula_weight	1618.1 kDa
Source method src_method	syn
Copy count entity_count	24

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F,H,J,L,N,P,Q,R,S,U,V,X,Z,a,b,c,d,f,g,h,i,j

XVXTTVLVVXVFV

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	nat
Copy count entity_count	20

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	575

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6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

Domain ID domain_id	6pbsA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1780 — Double Clp-N motif
Homologous superfamily homologous superfamily	10 — Clp, N-terminal domain

Domain ID domain_id	6pbsB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1780 — Double Clp-N motif
Homologous superfamily homologous superfamily	10 — Clp, N-terminal domain

Domain ID domain_id	6pbsC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1780 — Double Clp-N motif
Homologous superfamily homologous superfamily	10 — Clp, N-terminal domain

Domain ID domain_id	6pbsG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1780 — Double Clp-N motif
Homologous superfamily homologous superfamily	10 — Clp, N-terminal domain

Domain ID domain_id	6pbsI00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1780 — Double Clp-N motif
Homologous superfamily homologous superfamily	10 — Clp, N-terminal domain

Domain ID domain_id	6pbsK00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1780 — Double Clp-N motif
Homologous superfamily homologous superfamily	10 — Clp, N-terminal domain

Domain ID domain_id	6pbsO00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1780 — Double Clp-N motif
Homologous superfamily homologous superfamily	10 — Clp, N-terminal domain

Domain ID domain_id	6pbsT00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1780 — Double Clp-N motif
Homologous superfamily homologous superfamily	10 — Clp, N-terminal domain

Domain ID domain_id	6pbsW00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1780 — Double Clp-N motif
Homologous superfamily homologous superfamily	10 — Clp, N-terminal domain

Domain ID domain_id	6pbsY00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1780 — Double Clp-N motif
Homologous superfamily homologous superfamily	10 — Clp, N-terminal domain

Domain ID domain_id	6pbse00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1780 — Double Clp-N motif
Homologous superfamily homologous superfamily	10 — Clp, N-terminal domain

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Unit-cell length a length_a	80.063 Å
Unit-cell length b length_b	130.342 Å
Unit-cell length c length_c	112.562 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.07 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	—
R_work r_work	0.1800
R_free r_free	0.2570

Structure of ClpC1-NTD in complex with Ecumicin

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

ATP-dependent Clp protease ATP-binding subunit ClpC1

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

6pbs__assembly_1__model_1

6pbs__assembly_1__model_1 | I(q)

6pbs__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

7. Citations (1)

Structure of ClpC1-NTD in complex with Ecumicin

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

ATP-dependent Clp protease ATP-binding subunit ClpC1

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

6pbs__assembly_1__model_1

6pbs__assembly_1__model_1 | I(q)

6pbs__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

7. Citations (1)