8QZI | pdb_00008qzi

Crystal structure of PptT-ACP from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb8QZI/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-10-27 Released: 2024-06-19
Deposition Author(s): Gavalda, S., Mourey, L., Pedelacq, J.D.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.241 (Depositor), 0.247 (DCC)
R-Value Work:
0.196 (Depositor), 0.198 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Catalytic Cycle of Type II 4'-Phosphopantetheinyl Transferases

Gavalda, S., Faille, A., Fioccola, S., Nguyen, M.C., Carivenc, C., Rottier, K., Rufin, Y., Saitta, S., Czaplicki, G., Guilhot, C., Chalut, C., Brut, M., Mourey, L., Pedelacq, J.D.

(2024) ACS Catal 14: 8561-8575

DOI: https://doi.org/10.1021/acscatal.3c06249

Macromolecule Content

Total Structure Weight: 148.4 kDa
Atom Count: 8,389
Modeled Residue Count: 1,074
Deposited Residue Count: 1,332
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4'-phosphopantetheinyl transferase PptT	A, B, C, D	247	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: pptT EC: 2.7.8.7
UniProt
Find proteins for O33336 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O33336 Go to UniProtKB: O33336
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O33336
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenolphthiocerol/phthiocerol polyketide synthase subunit C	E, F	172	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: ppsC, Rv2933 EC: 2.3.1.292
UniProt
Find proteins for P96202 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P96202 Go to UniProtKB: P96202
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P96202
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA (Subject of Investigation/LOI) Query on COA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain Q [auth D] SDF format, chain M [auth C] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain G [auth A]	G [auth A], J [auth B], M [auth C], Q [auth D]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D]
IPA (Subject of Investigation/LOI) Query on IPA Download:Ideal Coordinates CCD File SDF format, chain T [auth E] SDF format, chain P [auth C] MOL2 format, chain T [auth E] MOL2 format, chain P [auth C] mmCIF format, chain T [auth E] mmCIF format, chain P [auth C]	P [auth C], T [auth E]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Focus chain T [auth E] Interactions & Density Focus chain P [auth C] Focus chain T [auth E]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] K [auth B] L [auth B] N [auth C] H [auth A], I [auth A], K [auth B], L [auth B], N [auth C], O [auth C], R [auth D], S [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D]