9JOP | pdb_00009jop

Caseinolytic protease P from bacteria

PDB DOI: https://doi.org/10.2210/pdb9JOP/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-25 Released: 2025-12-31
Deposition Author(s): Lu, M., Yin, J., Xiao, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.238 (Depositor), 0.239 (DCC)
R-Value Work:
0.201 (Depositor), 0.203 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Caseinolytic protease P from bacteria

Lu, M., Yin, J., Xiao, Y.

To be published.

Macromolecule Content

Total Structure Weight: 157.29 kDa
Atom Count: 10,697
Modeled Residue Count: 1,337
Deposited Residue Count: 1,372
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 [auth H] B [auth I] C [auth J] D [auth K] E [auth L] A [auth H], B [auth I], C [auth J], D [auth K], E [auth L], F [auth M], G [auth N]	196	Staphylococcus aureus	Mutation(s): 0 Gene Names: clpP_1, clpP, clpP_2, AC807_1014, AS572_03440, BN1321_180012, C0100_005090, CFN12_03925, CV021_05845, DQV00_11880... clpP_1, clpP, clpP_2, AC807_1014, AS572_03440, BN1321_180012, C0100_005090, CFN12_03925, CV021_05845, DQV00_11880, E1948_01285, E1948_03940, EIG96_02200, EP54_12650, EQ90_03850, ERS092965_00233, ERS1058648_00327, ERS195417_01014, G0V59_06660, G0Z31_01560, G6W84_01590, G6Y24_04455, GO793_13920, GO814_03290, GO942_03115, GQX37_00485, GQX52_02445, GZ156_04030, HT539_03325, M1K003_1188, NCTC10702_01301, NCTC13131_00808, NCTC5664_02933, NCTC7878_03438, NCTC7972_01134, QU38_10910, SAMEA1029519_00045, SAMEA1531725_00893, SAMEA1965892_01470, SAMEA2078260_01084, SAMEA2078588_00822, SAMEA2079512_00327, SAMEA2080344_01058, SAMEA2080909_01104, SAMEA2081063_00578, SAMEA2081779_01489, SAMEA4008452_00326, SAMEA4008575_00328, SAMEA4008601_00337, SAMEA4008627_00261, SAMEA4552975_01051, SAMEA70146418_00708, SAMEA70153168_02138, SAMEA70245418_01774 EC: 3.4.21.92
UniProt
Find proteins for A0A0D1I3W4 (Staphylococcus aureus) Explore A0A0D1I3W4 Go to UniProtKB: A0A0D1I3W4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0D1I3W4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EDS Query on A1EDS Download Ideal Coordinates CCD File SDF format, chain DA [auth L] SDF format, chain GA [auth M] SDF format, chain K [auth H] SDF format, chain LA [auth N] SDF format, chain P [auth I] SDF format, chain T [auth J] SDF format, chain Y [auth K] MOL2 format, chain DA [auth L] MOL2 format, chain GA [auth M] MOL2 format, chain K [auth H] MOL2 format, chain LA [auth N] MOL2 format, chain P [auth I] MOL2 format, chain T [auth J] MOL2 format, chain Y [auth K] mmCIF format, chain DA [auth L] mmCIF format, chain GA [auth M] mmCIF format, chain K [auth H] mmCIF format, chain LA [auth N] mmCIF format, chain P [auth I] mmCIF format, chain T [auth J] mmCIF format, chain Y [auth K]	DA [auth L] GA [auth M] K [auth H] LA [auth N] P [auth I] DA [auth L], GA [auth M], K [auth H], LA [auth N], P [auth I], T [auth J], Y [auth K]	(12~{R})-7-[(4-chlorophenyl)methyl]-12-(ethoxymethyl)-11-[(3-fluorophenyl)methyl]-2,5,7,11-tetrazatricyclo[7.4.0.0^{2,6}]trideca-1(9),5-dien-8-one C₂₆ H₂₈ Cl F N₄ O₂ VCPJLNSMEZPNKY-JOCHJYFZSA-N		Interactions Focus chain DA [auth L] Focus chain GA [auth M] Focus chain K [auth H] Focus chain LA [auth N] Focus chain P [auth I] Focus chain T [auth J] Focus chain Y [auth K] Interactions & Density Focus chain DA [auth L] Focus chain GA [auth M] Focus chain K [auth H] Focus chain LA [auth N] Focus chain P [auth I] Focus chain T [auth J] Focus chain Y [auth K]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth L] SDF format, chain BA [auth L] SDF format, chain CA [auth L] SDF format, chain EA [auth M] SDF format, chain FA [auth M] SDF format, chain H SDF format, chain HA [auth N] SDF format, chain I [auth H] SDF format, chain IA [auth N] SDF format, chain J [auth H] SDF format, chain JA [auth N] SDF format, chain KA [auth N] SDF format, chain L [auth I] SDF format, chain M [auth I] SDF format, chain N [auth I] SDF format, chain O [auth I] SDF format, chain Q [auth J] SDF format, chain R [auth J] SDF format, chain S [auth J] SDF format, chain U [auth K] SDF format, chain V [auth K] SDF format, chain W [auth K] SDF format, chain X [auth K] SDF format, chain Z [auth L] MOL2 format, chain AA [auth L] MOL2 format, chain BA [auth L] MOL2 format, chain CA [auth L] MOL2 format, chain EA [auth M] MOL2 format, chain FA [auth M] MOL2 format, chain H MOL2 format, chain HA [auth N] MOL2 format, chain I [auth H] MOL2 format, chain IA [auth N] MOL2 format, chain J [auth H] MOL2 format, chain JA [auth N] MOL2 format, chain KA [auth N] MOL2 format, chain L [auth I] MOL2 format, chain M [auth I] MOL2 format, chain N [auth I] MOL2 format, chain O [auth I] MOL2 format, chain Q [auth J] MOL2 format, chain R [auth J] MOL2 format, chain S [auth J] MOL2 format, chain U [auth K] MOL2 format, chain V [auth K] MOL2 format, chain W [auth K] MOL2 format, chain X [auth K] MOL2 format, chain Z [auth L] mmCIF format, chain AA [auth L] mmCIF format, chain BA [auth L] mmCIF format, chain CA [auth L] mmCIF format, chain EA [auth M] mmCIF format, chain FA [auth M] mmCIF format, chain H mmCIF format, chain HA [auth N] mmCIF format, chain I [auth H] mmCIF format, chain IA [auth N] mmCIF format, chain J [auth H] mmCIF format, chain JA [auth N] mmCIF format, chain KA [auth N] mmCIF format, chain L [auth I] mmCIF format, chain M [auth I] mmCIF format, chain N [auth I] mmCIF format, chain O [auth I] mmCIF format, chain Q [auth J] mmCIF format, chain R [auth J] mmCIF format, chain S [auth J] mmCIF format, chain U [auth K] mmCIF format, chain V [auth K] mmCIF format, chain W [auth K] mmCIF format, chain X [auth K] mmCIF format, chain Z [auth L]	AA [auth L] BA [auth L] CA [auth L] EA [auth M] FA [auth M] AA [auth L], BA [auth L], CA [auth L], EA [auth M], FA [auth M], H, HA [auth N], I [auth H], IA [auth N], J [auth H], JA [auth N], KA [auth N], L [auth I], M [auth I], N [auth I], O [auth I], Q [auth J], R [auth J], S [auth J], U [auth K], V [auth K], W [auth K], X [auth K], Z [auth L]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth L] Focus chain BA [auth L] Focus chain CA [auth L] Focus chain EA [auth M] Focus chain FA [auth M] Focus chain H Focus chain HA [auth N] Focus chain I [auth H] Focus chain IA [auth N] Focus chain J [auth H] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain L [auth I] Focus chain M [auth I] Focus chain N [auth I] Focus chain O [auth I] Focus chain Q [auth J] Focus chain R [auth J] Focus chain S [auth J] Focus chain U [auth K] Focus chain V [auth K] Focus chain W [auth K] Focus chain X [auth K] Focus chain Z [auth L] Interactions & Density Focus chain AA [auth L] Focus chain BA [auth L] Focus chain CA [auth L] Focus chain EA [auth M] Focus chain FA [auth M] Focus chain H Focus chain HA [auth N] Focus chain I [auth H] Focus chain IA [auth N] Focus chain J [auth H] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain L [auth I] Focus chain M [auth I] Focus chain N [auth I] Focus chain O [auth I] Focus chain Q [auth J] Focus chain R [auth J] Focus chain S [auth J] Focus chain U [auth K] Focus chain V [auth K] Focus chain W [auth K] Focus chain X [auth K] Focus chain Z [auth L]