PDB-9k2k: Structure of ClpP from Staphylococcus aureus in complex with ZY7

ID or keywords:

Entry

Database: PDB / ID: 9k2k

Title

Structure of ClpP from Staphylococcus aureus in complex with ZY7

Components

ATP-dependent Clp protease proteolytic subunit

Keywords

ANTIBIOTIC / ClpP / Staphylococcus aureus / activator / protease / HYDROLASE

Function / homology

Function and homology information

endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / cytoplasm
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.74 Å

Authors

Li, J.H. / Wu, W. / Zhang, T. / Yang, C.-G.

Funding support

China, 3items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)	22037007	China
National Natural Science Foundation of China (NSFC)	22107109	China
National Natural Science Foundation of China (NSFC)	22307029	China

Citation

Journal: J.Med.Chem. / Year: 2025
Title: Structure-Guided Development of ClpP Agonists with Potent Therapeutic Activities against Staphylococcus aureus Infection.
Authors: Zhang, T. / Wu, W. / Zhao, Y. / Ding, Z. / Wei, B. / Yang, T. / Li, J. / Wang, P. / Lan, L. / Gan, J. / Yang, C.G.

History

Deposition	Oct 17, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Feb 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9k2k.cif.gz	504.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9k2k.ent.gz		Display	PDB format
PDBx/mmJSON format	9k2k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k2/9k2k ftp://data.pdbj.org/pub/pdb/validation_reports/k2/9k2k	HTTPS FTP

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Related structure data

Related structure data	9k2aC 9k2bC 9k2cC 9k2dC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ATP-dependent Clp protease proteolytic subunit

B: ATP-dependent Clp protease proteolytic subunit

C: ATP-dependent Clp protease proteolytic subunit

D: ATP-dependent Clp protease proteolytic subunit

E: ATP-dependent Clp protease proteolytic subunit

F: ATP-dependent Clp protease proteolytic subunit

G: ATP-dependent Clp protease proteolytic subunit

H: ATP-dependent Clp protease proteolytic subunit

I: ATP-dependent Clp protease proteolytic subunit

J: ATP-dependent Clp protease proteolytic subunit

K: ATP-dependent Clp protease proteolytic subunit

L: ATP-dependent Clp protease proteolytic subunit

M: ATP-dependent Clp protease proteolytic subunit

N: ATP-dependent Clp protease proteolytic subunit

hetero molecules

320 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	96.368, 174.507, 194.455
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

#1: Protein	ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp Mass: 22365.414 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain Mu3 / ATCC 700698) (bacteria) Gene: clpP, SAHV_0765 / Production host: Escherichia coli (E. coli) / References: UniProt: A7WZR9, endopeptidase Clp
#2: Chemical	ChemComp-A1EEG / (6~{S},9~{a}~{S})-6-(2-methylpropyl)-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-~{N}-(phenylmethyl)-3,6,9,9~{a}-tetrahydro-2~{H}-pyrazino[1,2-a]pyrimidine-1-carboxamide Mass: 498.616 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₃₀H₃₄N₄O₃ / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.61 Å³/Da / Density % sol: 52.89 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium chloride, 0.1 M BICINE pH9.0, 20% PEG monomethyl ether 550

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 0.988 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.988 Å / Relative weight: 1

Reflection

Resolution: 2.74→129.88 Å / Num. obs: 62269 / % possible obs: 92.4 % / Redundancy: 4 % / CC_1/2: 0.993 / CC star: 0.998 / R_merge(I) obs: 0.079 / R_pim(I) all: 0.039 / R_rim(I) all: 0.088 / Χ²: 1.994 / Net I/σ(I): 11.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.75-2.85	2.4	0.273	5356	0.566	0.85	0.19	0.336	1.072	82.2
2.85-2.96	2.6	0.232	5559	0.741	0.923	0.154	0.281	1.152	85.4
2.96-3.1	2.8	0.199	5711	0.867	0.964	0.124	0.236	1.267	87.5
3.1-3.26	2.9	0.16	5706	0.926	0.981	0.099	0.19	1.404	87.4
3.26-3.46	3.7	0.134	6114	0.969	0.992	0.073	0.154	1.492	93.7
3.46-3.73	4.3	0.107	6297	0.985	0.996	0.053	0.12	1.731	96.3
3.73-4.11	4.6	0.085	6357	0.992	0.998	0.041	0.094	1.951	97.4
4.11-4.7	4.9	0.07	6425	0.994	0.999	0.033	0.077	2.42	97.9
4.7-5.91	5.3	0.072	6428	0.994	0.999	0.033	0.079	2.383	97.9
5.91-30	5.8	0.056	6551	0.998	0.999	0.024	0.061	2.69	98.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
HKL-2000		data scaling
autoPROC		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.74→129.88 Å / Cor.coef. F_o:F_c: 0.903 / Cor.coef. F_o:F_c free: 0.879 / SU B: 19.099 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24868	3410	5.2 %	RANDOM
R_work	0.22558	-	-	-
obs	0.22678	62269	75.79 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 49.868 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.14 Å²	0 Å²	0 Å²
2-	-	1.87 Å²	-0 Å²
3-	-	-	-4.01 Å²

Refinement step

Cycle: 1 / Resolution: 2.74→129.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20112	0	518	0	20630

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	20975
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	20454
X-RAY DIFFRACTION	r_angle_refined_deg	1.644	2.002	28375
X-RAY DIFFRACTION	r_angle_other_deg	1.482	3	47045
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.838	5	2602
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.197	25.515	903
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.007	15	3704
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.881	15	104
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	3255
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	23682
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	4490
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.936	4.868	10474
X-RAY DIFFRACTION	r_mcbond_other	2.934	4.867	10473
X-RAY DIFFRACTION	r_mcangle_it	4.756	7.293	13054
X-RAY DIFFRACTION	r_mcangle_other	4.756	7.294	13055
X-RAY DIFFRACTION	r_scbond_it	3.103	5.148	10501
X-RAY DIFFRACTION	r_scbond_other	3.102	5.148	10502
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.166	7.611	15322
X-RAY DIFFRACTION	r_long_range_B_refined	7.205	37.756	22330
X-RAY DIFFRACTION	r_long_range_B_other	7.204	37.756	22331
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	22542	0.05
1	2	B	22542	0.05
2	1	A	22468	0.05
2	2	C	22468	0.05
3	1	A	22182	0.06
3	2	D	22182	0.06
4	1	A	22328	0.05
4	2	E	22328	0.05
5	1	A	22414	0.06
5	2	F	22414	0.06
6	1	A	22402	0.06
6	2	G	22402	0.06
7	1	A	22582	0.03
7	2	H	22582	0.03
8	1	A	22462	0.04
8	2	I	22462	0.04
9	1	A	22602	0.05
9	2	J	22602	0.05
10	1	A	22252	0.06
10	2	K	22252	0.06
11	1	A	22314	0.06
11	2	L	22314	0.06
12	1	A	22386	0.05
12	2	M	22386	0.05
13	1	A	22274	0.05
13	2	N	22274	0.05
14	1	B	22504	0.05
14	2	C	22504	0.05
15	1	B	22236	0.05
15	2	D	22236	0.05
16	1	B	22380	0.04
16	2	E	22380	0.04
17	1	B	22460	0.05
17	2	F	22460	0.05
18	1	B	22438	0.05
18	2	G	22438	0.05
19	1	B	22430	0.04
19	2	H	22430	0.04
20	1	B	22472	0.04
20	2	I	22472	0.04
21	1	B	22782	0.04
21	2	J	22782	0.04
22	1	B	22308	0.05
22	2	K	22308	0.05
23	1	B	22362	0.05
23	2	L	22362	0.05
24	1	B	22428	0.04
24	2	M	22428	0.04
25	1	B	22360	0.05
25	2	N	22360	0.05
26	1	C	22466	0.05
26	2	D	22466	0.05
27	1	C	22236	0.05
27	2	E	22236	0.05
28	1	C	22326	0.05
28	2	F	22326	0.05
29	1	C	22242	0.06
29	2	G	22242	0.06
30	1	C	22380	0.04
30	2	H	22380	0.04
31	1	C	22402	0.04
31	2	I	22402	0.04
32	1	C	22636	0.04
32	2	J	22636	0.04
33	1	C	22374	0.05
33	2	K	22374	0.05
34	1	C	22380	0.05
34	2	L	22380	0.05
35	1	C	22296	0.05
35	2	M	22296	0.05
36	1	C	22126	0.06
36	2	N	22126	0.06
37	1	D	22754	0.05
37	2	E	22754	0.05
38	1	D	22624	0.06
38	2	F	22624	0.06
39	1	D	22528	0.06
39	2	G	22528	0.06
40	1	D	22196	0.05
40	2	H	22196	0.05
41	1	D	22022	0.05
41	2	I	22022	0.05
42	1	D	22478	0.06
42	2	J	22478	0.06
43	1	D	22754	0.05
43	2	K	22754	0.05
44	1	D	22816	0.04
44	2	L	22816	0.04
45	1	D	22716	0.05
45	2	M	22716	0.05
46	1	D	22286	0.05
46	2	N	22286	0.05
47	1	E	22978	0.04
47	2	F	22978	0.04
48	1	E	22742	0.05
48	2	G	22742	0.05
49	1	E	22270	0.04
49	2	H	22270	0.04
50	1	E	22102	0.05
50	2	I	22102	0.05
51	1	E	22692	0.05
51	2	J	22692	0.05
52	1	E	22856	0.04
52	2	K	22856	0.04
53	1	E	22856	0.04
53	2	L	22856	0.04
54	1	E	23128	0.04
54	2	M	23128	0.04
55	1	E	22546	0.04
55	2	N	22546	0.04
56	1	F	22862	0.04
56	2	G	22862	0.04
57	1	F	22344	0.04
57	2	H	22344	0.04
58	1	F	22208	0.05
58	2	I	22208	0.05
59	1	F	22800	0.05
59	2	J	22800	0.05
60	1	F	22742	0.05
60	2	K	22742	0.05
61	1	F	22914	0.05
61	2	L	22914	0.05
62	1	F	22998	0.04
62	2	M	22998	0.04
63	1	F	22644	0.04
63	2	N	22644	0.04
64	1	G	22266	0.05
64	2	H	22266	0.05
65	1	G	22146	0.05
65	2	I	22146	0.05
66	1	G	22668	0.05
66	2	J	22668	0.05
67	1	G	22640	0.05
67	2	K	22640	0.05
68	1	G	22744	0.04
68	2	L	22744	0.04
69	1	G	22782	0.04
69	2	M	22782	0.04
70	1	G	22486	0.04
70	2	N	22486	0.04
71	1	H	22408	0.04
71	2	I	22408	0.04
72	1	H	22534	0.03
72	2	J	22534	0.03
73	1	H	22230	0.05
73	2	K	22230	0.05
74	1	H	22244	0.05
74	2	L	22244	0.05
75	1	H	22330	0.04
75	2	M	22330	0.04
76	1	H	22182	0.05
76	2	N	22182	0.05
77	1	I	22512	0.04
77	2	J	22512	0.04
78	1	I	22190	0.05
78	2	K	22190	0.05
79	1	I	22110	0.05
79	2	L	22110	0.05
80	1	I	22156	0.04
80	2	M	22156	0.04
81	1	I	22202	0.05
81	2	N	22202	0.05
82	1	J	22638	0.06
82	2	K	22638	0.06
83	1	J	22648	0.05
83	2	L	22648	0.05
84	1	J	22710	0.05
84	2	M	22710	0.05
85	1	J	22428	0.04
85	2	N	22428	0.04
86	1	K	22886	0.03
86	2	L	22886	0.03
87	1	K	22766	0.05
87	2	M	22766	0.05
88	1	K	22350	0.05
88	2	N	22350	0.05
89	1	L	22806	0.04
89	2	M	22806	0.04
90	1	L	22432	0.04
90	2	N	22432	0.04
91	1	M	22600	0.04
91	2	N	22600	0.04

LS refinement shell

Resolution: 2.742→2.813 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.369	178	-
R_work	0.358	3336	-
obs	-	-	55.5 %

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