9IF4 | pdb_00009if4

Structure of the Mycobacterium Tuberculosis ClpC1P1P2 complex bound to the activator Bz-Leu-Leu

PDB DOI: https://doi.org/10.2210/pdb9IF4/pdb
EM Map EMD-52840: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Mycobacterium tuberculosis, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-02-17 Released: 2025-08-27
Deposition Author(s): Weinhaeupl, K., Semchonok, D., Gragera, M., Arranz, R., Bueno Carrasco, M.T., Fraga, H.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.09 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of the Mycobacterium Tuberculosis ClpC1P1P2 complex bound to the activator Bz-Leu-Leu

Weinhaeupl, K., Semchonok, D.A., Gragera, M., Arranz, R., Bueno Carrasco, M.T., Fraga, H.

To be published.

Macromolecule Content

Total Structure Weight: 741.77 kDa
Atom Count: 45,182
Modeled Residue Count: 5,762
Deposited Residue Count: 6,641
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease ATP-binding subunit ClpC1	A, B, C, D, E A, B, C, D, E, F	658	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: clpC1, Rv3596c, MTCY07H7B.26
UniProt
Find proteins for P9WPC9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPC9 Go to UniProtKB: P9WPC9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WPC9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit 2	G H I J K [auth L] G, H, I, J, K [auth L], L [auth M], T [auth K]	200	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: clpP2, Rv2460c, MTV008.16c EC: 3.4.21.92
UniProt
Find proteins for P9WPC3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPC3 Go to UniProtKB: P9WPC3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WPC3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit 1	M [auth N] N [auth O] O [auth P] P [auth Q] Q [auth R] M [auth N], N [auth O], O [auth P], P [auth Q], Q [auth R], R [auth S], S [auth T]	179	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: clpP1, clpP, Rv2461c, MTV008.17c EC: 3.4.21.92
UniProt
Find proteins for P9WPC5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPC5 Go to UniProtKB: P9WPC5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WPC5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
activator Bz-Leu-Leu	AA [auth b] U V W X [auth Y] AA [auth b], U, V, W, X [auth Y], Y [auth Z], Z [auth a]	2	synthetic construct	Mutation(s): 0

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown peptide	BA [auth X]	26	Mycobacterium tuberculosis	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain LA [auth E] SDF format, chain KA [auth E] SDF format, chain JA [auth D] SDF format, chain IA [auth D] SDF format, chain HA [auth C] SDF format, chain GA [auth C] SDF format, chain FA [auth B] SDF format, chain EA [auth B] MOL2 format, chain LA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain JA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] mmCIF format, chain LA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain JA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B]	EA [auth B] FA [auth B] GA [auth C] HA [auth C] IA [auth D] EA [auth B], FA [auth B], GA [auth C], HA [auth C], IA [auth D], JA [auth D], KA [auth E], LA [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth E] Focus chain LA [auth E] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth E] Focus chain LA [auth E]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain NA [auth F] SDF format, chain MA [auth F] SDF format, chain DA [auth A] SDF format, chain CA [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain MA [auth F] MOL2 format, chain DA [auth A] MOL2 format, chain CA [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain MA [auth F] mmCIF format, chain DA [auth A] mmCIF format, chain CA [auth A]	CA [auth A], DA [auth A], MA [auth F], NA [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain CA [auth A] Focus chain DA [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Interactions & Density Focus chain CA [auth A] Focus chain DA [auth A] Focus chain MA [auth F] Focus chain NA [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
S0R Query on S0R	AA [auth b] U V W X [auth Y] AA [auth b], U, V, W, X [auth Y], Y [auth Z], Z [auth a]	L-PEPTIDE LINKING	C₁₃ H₁₇ N O₃		LEU
UNK Query on UNK	BA [auth X]	L-PEPTIDE LINKING	C₄ H₉ N O₂		--