8EF8 | pdb_00008ef8

Staphylococcus aureus ClpP Y63W in complex with compound 3471

PDB DOI: https://doi.org/10.2210/pdb8EF8/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-09-08 Released: 2023-07-19
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: 2.17 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.202 (Depositor), 0.200 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
View more details

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: 324.18 kDa
Atom Count: 20,744
Modeled Residue Count: 2,500
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): 1 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
USU (Subject of Investigation/LOI) Query on USU Download Ideal Coordinates CCD File SDF format, chain CA [auth I] SDF format, chain EA [auth K] SDF format, chain HA [auth M] SDF format, chain JA [auth N] SDF format, chain LA [auth S] SDF format, chain NA [auth T] SDF format, chain P [auth A] SDF format, chain R [auth B] 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 I] MOL2 format, chain EA [auth K] MOL2 format, chain HA [auth M] MOL2 format, chain JA [auth N] MOL2 format, chain LA [auth S] MOL2 format, chain NA [auth T] MOL2 format, chain P [auth A] MOL2 format, chain R [auth B] 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 I] mmCIF format, chain EA [auth K] mmCIF format, chain HA [auth M] mmCIF format, chain JA [auth N] mmCIF format, chain LA [auth S] mmCIF format, chain NA [auth T] mmCIF format, chain P [auth A] mmCIF format, chain R [auth B] 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 I] EA [auth K] HA [auth M] JA [auth N] LA [auth S] CA [auth I], EA [auth K], HA [auth M], JA [auth N], LA [auth S], NA [auth T], P [auth A], R [auth B], 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 I] Focus chain EA [auth K] Focus chain HA [auth M] Focus chain JA [auth N] Focus chain LA [auth S] Focus chain NA [auth T] Focus chain P [auth A] Focus chain R [auth B] 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 I] Focus chain EA [auth K] Focus chain HA [auth M] Focus chain JA [auth N] Focus chain LA [auth S] Focus chain NA [auth T] Focus chain P [auth A] Focus chain R [auth B] 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 I] SDF format, chain DA [auth K] SDF format, chain FA [auth L] SDF format, chain GA [auth M] SDF format, chain IA [auth N] SDF format, chain KA [auth S] SDF format, chain MA [auth T] SDF format, chain O [auth A] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain W [auth E] SDF format, chain Y [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth I] MOL2 format, chain DA [auth K] MOL2 format, chain FA [auth L] MOL2 format, chain GA [auth M] MOL2 format, chain IA [auth N] MOL2 format, chain KA [auth S] MOL2 format, chain MA [auth T] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Y [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth I] mmCIF format, chain DA [auth K] mmCIF format, chain FA [auth L] mmCIF format, chain GA [auth M] mmCIF format, chain IA [auth N] mmCIF format, chain KA [auth S] mmCIF format, chain MA [auth T] mmCIF format, chain O [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Y [auth F]	AA [auth G] BA [auth I] DA [auth K] FA [auth L] GA [auth M] AA [auth G], BA [auth I], DA [auth K], FA [auth L], GA [auth M], IA [auth N], KA [auth S], MA [auth T], O [auth A], Q [auth B], 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 I] Focus chain DA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain IA [auth N] Focus chain KA [auth S] Focus chain MA [auth T] Focus chain O [auth A] Focus chain Q [auth B] 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 I] Focus chain DA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain IA [auth N] Focus chain KA [auth S] Focus chain MA [auth T] Focus chain O [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain Y [auth F]