8E7P

Staphylococcus aureus ClpP in complex with compound 3421

PDB DOI: https://doi.org/10.2210/pdb8E7P/pdb

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

Deposited: 2022-08-24 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: 1.68 Å
R-Value Free: 0.182
R-Value Work: 0.166
R-Value Observed: 0.167

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: 325.41 kDa
Atom Count: 22,701
Modelled Residue Count: 2,537
Deposited Residue Count: 2,842
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2G036
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UTC (Subject of Investigation/LOI) Query on UTC Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain DA [auth I] SDF format, chain EA [auth K] SDF format, chain GA [auth L] SDF format, chain IA [auth M] SDF format, chain KA [auth N] SDF format, chain MA [auth S] SDF format, chain OA [auth S] SDF format, chain P [auth A] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain Y [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain DA [auth I] MOL2 format, chain EA [auth K] MOL2 format, chain GA [auth L] MOL2 format, chain IA [auth M] MOL2 format, chain KA [auth N] MOL2 format, chain MA [auth S] MOL2 format, chain OA [auth S] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain DA [auth I] mmCIF format, chain EA [auth K] mmCIF format, chain GA [auth L] mmCIF format, chain IA [auth M] mmCIF format, chain KA [auth N] mmCIF format, chain MA [auth S] mmCIF format, chain OA [auth S] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth F]	AA [auth G] DA [auth I] EA [auth K] GA [auth L] IA [auth M] AA [auth G], DA [auth I], EA [auth K], GA [auth L], IA [auth M], KA [auth N], MA [auth S], OA [auth S], P [auth A], Q [auth B], S [auth C], W [auth D], Y [auth F]	(5R,6S,9aS)-N-benzyl-6-[(4-hydroxyphenyl)methyl]-8-[(naphthalen-1-yl)methyl]-4,7-dioxohexahydro-2H-pyrazino[1,2-a]pyrimidine-1(6H)-carboxamide C₃₃ H₃₂ N₄ O₄ HQWTUOLCGKIECB-XZWHSSHBSA-N		Interactions Focus chain AA [auth G] Focus chain DA [auth I] Focus chain EA [auth K] Focus chain GA [auth L] Focus chain IA [auth M] Focus chain KA [auth N] Focus chain MA [auth S] Focus chain OA [auth S] Focus chain P [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Y [auth F] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth I] Focus chain EA [auth K] Focus chain GA [auth L] Focus chain IA [auth M] Focus chain KA [auth N] Focus chain MA [auth S] Focus chain OA [auth S] Focus chain P [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Y [auth F]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain CA [auth I] SDF format, chain FA [auth K] SDF format, chain HA [auth L] SDF format, chain JA [auth M] SDF format, chain LA [auth N] SDF format, chain NA [auth S] SDF format, chain O [auth A] SDF format, chain PA [auth T] SDF format, chain R [auth B] SDF format, chain T [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain X [auth E] SDF format, chain Z [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain CA [auth I] MOL2 format, chain FA [auth K] MOL2 format, chain HA [auth L] MOL2 format, chain JA [auth M] MOL2 format, chain LA [auth N] MOL2 format, chain NA [auth S] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth T] MOL2 format, chain R [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain BA [auth G] mmCIF format, chain CA [auth I] mmCIF format, chain FA [auth K] mmCIF format, chain HA [auth L] mmCIF format, chain JA [auth M] mmCIF format, chain LA [auth N] mmCIF format, chain NA [auth S] mmCIF format, chain O [auth A] mmCIF format, chain PA [auth T] mmCIF format, chain R [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain X [auth E] mmCIF format, chain Z [auth F]	BA [auth G] CA [auth I] FA [auth K] HA [auth L] JA [auth M] BA [auth G], CA [auth I], FA [auth K], HA [auth L], JA [auth M], LA [auth N], NA [auth S], O [auth A], PA [auth T], R [auth B], T [auth C], U [auth D], V [auth D], X [auth E], Z [auth F]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain BA [auth G] Focus chain CA [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 PA [auth T] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth E] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth G] Focus chain CA [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 PA [auth T] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth E] Focus chain Z [auth F]