6NB1 | pdb_00006nb1

Crystal structure of Escherichia coli ClpP protease complexed with small molecule activator, ACP1-06

PDB DOI: https://doi.org/10.2210/pdb6NB1/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-12-06 Released: 2019-11-13
Deposition Author(s): Mabanglo, M.F., Houry, W.A., Eger, B.T., Bryson, S., Pai, E.F.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.244 (Depositor), 0.250 (DCC)
R-Value Work:
0.209 (Depositor), 0.218 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores.

Mabanglo, M.F., Leung, E., Vahidi, S., Seraphim, T.V., Eger, B.T., Bryson, S., Bhandari, V., Zhou, J.L., Mao, Y.Q., Rizzolo, K., Barghash, M.M., Goodreid, J.D., Phanse, S., Babu, M., Barbosa, L.R.S., Ramos, C.H.I., Batey, R.A., Kay, L.E., Pai, E.F., Houry, W.A.

(2019) Commun Biol 2: 410-410

DOI: https://doi.org/10.1038/s42003-019-0656-3

Macromolecule Content

Total Structure Weight: 332.8 kDa
Atom Count: 21,848
Modeled Residue Count: 2,561
Deposited Residue Count: 2,898
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, I, J, K, L, M, N	207	Escherichia coli K-12	Mutation(s): 0 Gene Names: clpP, lopP, b0437, JW0427 EC: 3.4.21.92
UniProt
Find proteins for P0A6G7 (Escherichia coli (strain K12)) Explore P0A6G7 Go to UniProtKB: P0A6G7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6G7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KHS Query on KHS Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain CA [auth H] SDF format, chain EA [auth I] SDF format, chain GA [auth J] SDF format, chain IA [auth K] SDF format, chain KA [auth L] SDF format, chain MA [auth M] SDF format, chain O [auth A] SDF format, chain OA [auth N] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain Y [auth F] SDF format, chain W [auth E] MOL2 format, chain AA [auth G] MOL2 format, chain CA [auth H] MOL2 format, chain EA [auth I] MOL2 format, chain GA [auth J] MOL2 format, chain IA [auth K] MOL2 format, chain KA [auth L] MOL2 format, chain MA [auth M] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth N] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth F] MOL2 format, chain W [auth E] mmCIF format, chain AA [auth G] mmCIF format, chain CA [auth H] mmCIF format, chain EA [auth I] mmCIF format, chain GA [auth J] mmCIF format, chain IA [auth K] mmCIF format, chain KA [auth L] mmCIF format, chain MA [auth M] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth N] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain Y [auth F] mmCIF format, chain W [auth E]	AA [auth G] CA [auth H] EA [auth I] GA [auth J] IA [auth K] AA [auth G], CA [auth H], EA [auth I], GA [auth J], IA [auth K], KA [auth L], MA [auth M], O [auth A], OA [auth N], Q [auth B], S [auth C], U [auth D], W [auth E], Y [auth F]	N-{2-[(2-chlorophenyl)sulfanyl]ethyl}-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]sulfonyl}propanamide C₁₈ H₁₈ Cl F₃ N₂ O₃ S₂ OUZIIFOEMPAZKX-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain CA [auth H] Focus chain EA [auth I] Focus chain GA [auth J] Focus chain IA [auth K] Focus chain KA [auth L] Focus chain MA [auth M] Focus chain O [auth A] Focus chain OA [auth N] 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 CA [auth H] Focus chain EA [auth I] Focus chain GA [auth J] Focus chain IA [auth K] Focus chain KA [auth L] Focus chain MA [auth M] Focus chain O [auth A] Focus chain OA [auth N] 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]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain FA [auth I] SDF format, chain HA [auth J] SDF format, chain JA [auth K] SDF format, chain LA [auth L] SDF format, chain NA [auth M] SDF format, chain PA [auth N] SDF format, chain T [auth C] SDF format, chain V [auth D] SDF format, chain X [auth E] SDF format, chain Z [auth F] SDF format, chain R [auth B] SDF format, chain P [auth A] SDF format, chain DA [auth H] MOL2 format, chain BA [auth G] MOL2 format, chain FA [auth I] MOL2 format, chain HA [auth J] MOL2 format, chain JA [auth K] MOL2 format, chain LA [auth L] MOL2 format, chain NA [auth M] MOL2 format, chain PA [auth N] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain R [auth B] MOL2 format, chain P [auth A] MOL2 format, chain DA [auth H] mmCIF format, chain BA [auth G] mmCIF format, chain FA [auth I] mmCIF format, chain HA [auth J] mmCIF format, chain JA [auth K] mmCIF format, chain LA [auth L] mmCIF format, chain NA [auth M] mmCIF format, chain PA [auth N] mmCIF format, chain T [auth C] mmCIF format, chain V [auth D] mmCIF format, chain X [auth E] mmCIF format, chain Z [auth F] mmCIF format, chain R [auth B] mmCIF format, chain P [auth A] mmCIF format, chain DA [auth H]	BA [auth G] DA [auth H] FA [auth I] HA [auth J] JA [auth K] BA [auth G], DA [auth H], FA [auth I], HA [auth J], JA [auth K], LA [auth L], NA [auth M], P [auth A], PA [auth N], R [auth B], T [auth C], V [auth D], X [auth E], Z [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain DA [auth H] Focus chain FA [auth I] Focus chain HA [auth J] Focus chain JA [auth K] Focus chain LA [auth L] Focus chain NA [auth M] Focus chain P [auth A] Focus chain PA [auth N] 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 BA [auth G] Focus chain DA [auth H] Focus chain FA [auth I] Focus chain HA [auth J] Focus chain JA [auth K] Focus chain LA [auth L] Focus chain NA [auth M] Focus chain P [auth A] Focus chain PA [auth N] 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.244 (Depositor), 0.250 (DCC)
R-Value Work: 0.209 (Depositor), 0.218 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.985	α = 90
b = 101.094	β = 98.29
c = 155.194	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-11-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	XNE-86945
Canadian Institutes of Health Research (CIHR)	Canada	PJT-148564

Revision History (Full details and data files)

Version 1.0: 2019-11-13
Type: Initial release
Version 1.1: 2020-01-08
Changes: Author supporting evidence
Version 1.2: 2020-01-29
Changes: Database references
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Refinement description