4u0g

Crystal Structure of M. tuberculosis ClpP1P2 bound to ADEP and agonist

Method: X-RAY DIFFRACTION

▼

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

ATP-dependent Clp protease proteolytic subunit 2

Mycobacterium tuberculosis H37Rv

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 21	ATP-dependent Clp protease proteolytic subunit 1 × 7 （P9WPC5） ADEP-2B5Me × 7 N-[(benzyloxy)carbonyl]-L-isoleucyl-L-leucine × 14 SULFATE ION × 17 DIMETHYL SULFOXIDE × 8 (2E,5S)-5-methylhept-2-enoic acid × 7 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 21	ATP-dependent Clp protease proteolytic subunit 1 × 7 （P9WPC5） ADEP-2B5Me × 7 N-[(benzyloxy)carbonyl]-L-isoleucyl-L-leucine × 14 SULFATE ION × 18 DIMETHYL SULFOXIDE × 7 (2E,5S)-5-methylhept-2-enoic acid × 7 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CLPP2_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–202； UniProt 13–214 Author chain B； PDBConstruct 1–202； UniProt 13–214 Author chain C； PDBConstruct 1–202； UniProt 13–214 Author chain D； PDBConstruct 1–202； UniProt 13–214 Author chain E； PDBConstruct 1–202； UniProt 13–214 Author chain F； PDBConstruct 1–202； UniProt 13–214 Author chain G； PDBConstruct 1–202； UniProt 13–214 Author chain O； PDBConstruct 1–202； UniProt 13–214 Author chain P； PDBConstruct 1–202； UniProt 13–214 Author chain Q； PDBConstruct 1–202； UniProt 13–214 Author chain R； PDBConstruct 1–202； UniProt 13–214 Author chain S； PDBConstruct 1–202； UniProt 13–214 Author chain T； PDBConstruct 1–202； UniProt 13–214 Author chain U； PDBConstruct 1–202； UniProt 13–214

ATP-dependent Clp protease proteolytic subunit 1

Mycobacterium tuberculosis H37Rv

UniProt P9WPC5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 21	ATP-dependent Clp protease proteolytic subunit 2 × 7 （P9WPC3） ADEP-2B5Me × 7 N-[(benzyloxy)carbonyl]-L-isoleucyl-L-leucine × 14 SULFATE ION × 17 DIMETHYL SULFOXIDE × 8 (2E,5S)-5-methylhept-2-enoic acid × 7 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 21	ATP-dependent Clp protease proteolytic subunit 2 × 7 （P9WPC3） ADEP-2B5Me × 7 N-[(benzyloxy)carbonyl]-L-isoleucyl-L-leucine × 14 SULFATE ION × 18 DIMETHYL SULFOXIDE × 7 (2E,5S)-5-methylhept-2-enoic acid × 7 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CLPP1_MYCTU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 1–194； UniProt 7–200 Author chain I； PDBConstruct 1–194； UniProt 7–200 Author chain J； PDBConstruct 1–194； UniProt 7–200 Author chain K； PDBConstruct 1–194； UniProt 7–200 Author chain L； PDBConstruct 1–194； UniProt 7–200 Author chain M； PDBConstruct 1–194； UniProt 7–200 Author chain N； PDBConstruct 1–194； UniProt 7–200 Author chain V； PDBConstruct 1–194； UniProt 7–200 Author chain W； PDBConstruct 1–194； UniProt 7–200 Author chain X； PDBConstruct 1–194； UniProt 7–200 Author chain Y； PDBConstruct 1–194； UniProt 7–200 Author chain Z； PDBConstruct 1–194； UniProt 7–200 Author chain a； PDBConstruct 1–194； UniProt 7–200 Author chain b； PDBConstruct 1–194； UniProt 7–200

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_id	4u0g
Deposition date deposition_date	2014-07-11
Structure title title	Crystal Structure of M. tuberculosis ClpP1P2 bound to ADEP and agonist
Keywords keywords	hydrolase, peptidase, hydrolase-antibiotic complex; hydrolase/antibiotic
Experimental Method method	X-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.

4u0g__assembly_1__model_1

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

Download this curve (.dat)

4u0g__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4u0g__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.09 Å
Rg (electron density)	43.06 Å
Total Rg	43.46 Å
Atom count	40844
Residues	2567
Excluded volume	367840 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4u0g__assembly_1__model_1`	21-meric （21）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4u0g__assembly_2__model_1`	21-meric （21）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	ATP-dependent Clp protease proteolytic subunit 2
Molecular weight formula_weight	22235.3 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,O,P,Q,R,S,T,U
Atom count atom_count	81740

RYILPSFIEHSSFGVKESNPYNKLFEERIIFLGVQVDDASANDIMAQLLVLESLDPDRDITMYINSPGGGFTSLMAIYDTMQYVRADIQTVCLGQAASAAAVLLAAGTPGKRMALPNARVLIHQPSLSGVIQGQFSDLEIQAAEIERMRTLMETTLARHTGKDAGVIRKDTDRDKILTAEEAKDYGIIDTVLEYRKLSAQTA

Source Source

Source organism organism	Mycobacterium tuberculosis H37Rv
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	ATP-dependent Clp protease proteolytic subunit 1
Molecular weight formula_weight	21441.1 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	H,I,J,K,L,M,N,V,W,X,Y,Z,a,b

MRSNSQGLSLTDSVYERLLSERIIFLGSEVNDEIANRLCAQILLLAAEDASKDISLYINSPGGSISAGMAIYDTMVLAPCDIATYAMGMAASMGEFLLAAGTKGKRYALPHARILMHQPLGGVTGSAADIAIQAEQFAVIKKEMFRLNAEFTGQPIERIEADSDRDRWFTAAEALEYGFVDHIITRAHVNGEAQ

Source Source

Source organism organism	Mycobacterium tuberculosis H37Rv
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	ADEP-2B5Me
Molecular weight formula_weight	692.8 kDa
Source method src_method	syn
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	c,i,d,e,f,g,h,j,k,l,m,n,o,p

FTPXAP

Entity 4 Entity 4 non-polymer

Description description	N-[(benzyloxy)carbonyl]-L-isoleucyl-L-leucine
Molecular weight formula_weight	378.5 kDa
Source method src_method	syn
Copy count entity_count	28

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	35

Entity 6 Entity 6 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 7 Entity 7 non-polymer

Description description	(2E,5S)-5-methylhept-2-enoic acid
Molecular weight formula_weight	142.2 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

▼

6. Fold Classification (SCOP + CATH) 28 domains

CATH v4.4 (28 domains)

Domain ID domain_id	4u0gA00
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	4u0gB00
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	4u0gC00
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	4u0gD00
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	4u0gE00
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	4u0gF00
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	4u0gG00
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	4u0gH00
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	4u0gI00
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	4u0gJ00
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	4u0gK00
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	4u0gL00
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	4u0gM00
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	4u0gN00
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	4u0gO00
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	4u0gP00
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	4u0gQ00
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	4u0gR00
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	4u0gS00
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	4u0gT00
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	4u0gU00
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	4u0gV00
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	4u0gW00
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	4u0gX00
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	4u0gY00
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	4u0gZ00
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	4u0ga00
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	4u0gb00
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

▶

Unit-cell length a length_a	154.748 Å
Unit-cell length b length_b	187.673 Å
Unit-cell length c length_c	294.029 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.198 Å
Low-resolution limit resolution_low	49.913 Å
R factor r_factor	0.1919
R_work r_work	0.1903
R_free r_free	0.2223

Crystal Structure of M. tuberculosis ClpP1P2 bound to ADEP and agonist

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

ATP-dependent Clp protease proteolytic subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

ATP-dependent Clp protease proteolytic subunit 1

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

4u0g__assembly_1__model_1

4u0g__assembly_1__model_1 | I(q)

4u0g__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 28 domains

CATH v4.4 (28 domains)

7. Citations (1)

Crystal Structure of M. tuberculosis ClpP1P2 bound to ADEP and agonist

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

ATP-dependent Clp protease proteolytic subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP-dependent Clp protease proteolytic subunit 1

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

4u0g__assembly_1__model_1

4u0g__assembly_1__model_1 | I(q)

4u0g__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 28 domains

CATH v4.4 (28 domains)

7. Citations (1)