8E71 | pdb_00008e71

Staphylococcus aureus ClpP in complex with compound 3471

PDB DOI: https://doi.org/10.2210/pdb8E71/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-08-23 Released: 2023-07-05
Deposition Author(s): Lee, R.E., Griffith, E.C.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.171 (Depositor), 0.180 (DCC)
R-Value Work:
0.155 (Depositor), 0.168 (DCC)
R-Value Observed:
0.156 (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

Development of a high throughput and site specific, fluorescent polarization assay to screen for activators of Caseinolytic Protease P leads to the discovery of synthetically tractable new activator class

Singh, A.C., Zhao, Y., Griffith, E.C., Tangallapally, R., Jarret, M.W., Lee, R.E.

To be published.

Macromolecule Content

Total Structure Weight: 325.04 kDa
Atom Count: 22,593
Modeled Residue Count: 2,559
Deposited Residue Count: 2,842
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit	A B C D E A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth L], K [auth M], L [auth N], M [auth S], N [auth T]	203	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0 Gene Names: clpP, SAOUHSC_00790 EC: 3.4.21.92
UniProt
Find proteins for Q2G036 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G036 Go to UniProtKB: Q2G036
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2G036
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
USU (Subject of Investigation/LOI) Query on USU Download:Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain EA [auth I] SDF format, chain GA [auth K] SDF format, chain IA [auth L] SDF format, chain KA [auth M] SDF format, chain MA [auth N] SDF format, chain P [auth A] SDF format, chain PA [auth S] SDF format, chain R [auth B] SDF format, chain RA [auth T] SDF format, chain T [auth C] SDF format, chain V [auth D] SDF format, chain X [auth E] SDF format, chain Z [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain EA [auth I] MOL2 format, chain GA [auth K] MOL2 format, chain IA [auth L] MOL2 format, chain KA [auth M] MOL2 format, chain MA [auth N] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth S] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth T] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain EA [auth I] mmCIF format, chain GA [auth K] mmCIF format, chain IA [auth L] mmCIF format, chain KA [auth M] mmCIF format, chain MA [auth N] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth S] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth T] mmCIF format, chain T [auth C] mmCIF format, chain V [auth D] mmCIF format, chain X [auth E] mmCIF format, chain Z [auth F]	CA [auth G] EA [auth I] GA [auth K] IA [auth L] KA [auth M] CA [auth G], EA [auth I], GA [auth K], IA [auth L], KA [auth M], MA [auth N], P [auth A], PA [auth S], R [auth B], RA [auth T], T [auth C], V [auth D], X [auth E], Z [auth F]	(5S,6S,9aS)-N-[(4-fluorophenyl)methyl]-6-methyl-8-[(naphthalen-1-yl)methyl]-4,7-dioxohexahydro-2H-pyrazino[1,2-a]pyrimidine-1(6H)-carboxamide C₂₇ H₂₇ F N₄ O₃ UJSSMRPTIGCTEH-MHECFPHRSA-N		Interactions Focus chain CA [auth G] Focus chain EA [auth I] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain KA [auth M] Focus chain MA [auth N] Focus chain P [auth A] Focus chain PA [auth S] Focus chain R [auth B] Focus chain RA [auth T] Focus chain T [auth C] Focus chain V [auth D] Focus chain X [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain EA [auth I] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain KA [auth M] Focus chain MA [auth N] Focus chain P [auth A] Focus chain PA [auth S] Focus chain R [auth B] Focus chain RA [auth T] Focus chain T [auth C] Focus chain V [auth D] Focus chain X [auth E] Focus chain Z [auth F]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth G] SDF format, chain DA [auth I] SDF format, chain FA [auth K] SDF format, chain HA [auth L] SDF format, chain LA [auth N] SDF format, chain NA [auth S] SDF format, chain O [auth A] SDF format, chain OA [auth S] SDF format, chain Q [auth B] SDF format, chain QA [auth T] SDF format, chain U [auth D] SDF format, chain W [auth E] SDF format, chain Y [auth F] SDF format, chain S [auth C] SDF format, chain JA [auth M] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain DA [auth I] MOL2 format, chain FA [auth K] MOL2 format, chain HA [auth L] MOL2 format, chain LA [auth N] MOL2 format, chain NA [auth S] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth S] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth T] MOL2 format, chain U [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Y [auth F] MOL2 format, chain S [auth C] MOL2 format, chain JA [auth M] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain DA [auth I] mmCIF format, chain FA [auth K] mmCIF format, chain HA [auth L] mmCIF format, chain LA [auth N] mmCIF format, chain NA [auth S] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth S] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth T] mmCIF format, chain U [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Y [auth F] mmCIF format, chain S [auth C] mmCIF format, chain JA [auth M]	AA [auth G] BA [auth G] DA [auth I] FA [auth K] HA [auth L] AA [auth G], BA [auth G], DA [auth I], FA [auth K], HA [auth L], JA [auth M], LA [auth N], NA [auth S], O [auth A], OA [auth S], Q [auth B], QA [auth T], S [auth C], U [auth D], W [auth E], Y [auth F]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain DA [auth I] Focus chain FA [auth K] Focus chain HA [auth L] Focus chain JA [auth M] Focus chain LA [auth N] Focus chain NA [auth S] Focus chain O [auth A] Focus chain OA [auth S] Focus chain Q [auth B] Focus chain QA [auth T] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain Y [auth F] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain DA [auth I] Focus chain FA [auth K] Focus chain HA [auth L] Focus chain JA [auth M] Focus chain LA [auth N] Focus chain NA [auth S] Focus chain O [auth A] Focus chain OA [auth S] Focus chain Q [auth B] Focus chain QA [auth T] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain Y [auth F]