6NAH

Crystal structure of Neisseria meningitidis ClpP protease in complex with Acyldepsipeptide-14 (ADEP-14)

• PDB DOI: https://doi.org/10.2210/pdb6NAH/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Neisseria meningitidis, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-12-05 Released: 2019-11-13 
• Deposition Author(s): Mabanglo, M.F., Houry, W.A.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.248 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D7  (Explore in 3D)
Global Stoichiometry: Hetero 28-mer - A14B14 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 28-mer - A14B1C1D1E1F1G1H1I1J1K1L1M1N1O1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Dihedral - D7  (Explore in 3D)
Global Stoichiometry: Hetero 28-mer - A14B14 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 28-mer - A14B1C1D1E1F1G1H1I1J1K1L1M1N1O1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 706.94 kDa 
• Atom Count: 40,076 
• Modelled Residue Count: 5,007 
• Deposited Residue Count: 6,244 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit	A, AA [auth a], B, BA [auth b], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	217	Neisseria meningitidis	Mutation(s): 0  Gene Names: clpP EC: 3.4.21.92
UniProt
Find proteins for Q9JZ38 (Neisseria meningitidis serogroup B (strain MC58)) Explore Q9JZ38  Go to UniProtKB:  Q9JZ38

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyldepsipeptide-14	AB [auth 1], BB [auth 2], CA [auth c], CB [auth 3], DA [auth e], DB [auth 4], EA [auth f], FA [auth g], GA [auth h], HA [auth i], IA [auth j], JA [auth k], KA [auth l], LA [auth m], MA [auth n], NA [auth o], OA [auth p], PA [auth q], QA [auth r], RA [auth s], SA [auth t], TA [auth u], UA [auth v], VA [auth w], WA [auth x], XA [auth y], YA [auth z], ZA [auth 0]	6	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OCA	AC [auth z], BC [auth 0], CC [auth 1], DC [auth 2], EB [auth c], EC [auth 3], FB [auth e], FC [auth 4], GB [auth f], HB [auth g], IB [auth h], JB [auth i], KB [auth j], LB [auth k], MB [auth l], NB [auth m], OB [auth n], PB [auth o], QB [auth p], RB [auth q], SB [auth r], TB [auth s], UB [auth t], VB [auth u], WB [auth v], XB [auth w], YB [auth x], ZB [auth y]	OCTANOIC ACID (CAPRYLIC ACID) C8 H16 O2 WWZKQHOCKIZLMA-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALO	AB [auth 1], BB [auth 2], CA [auth c], CB [auth 3], DA [auth e], DB [auth 4], EA [auth f], FA [auth g], GA [auth h], HA [auth i], IA [auth j], JA [auth k], KA [auth l], LA [auth m], MA [auth n], NA [auth o], OA [auth p], PA [auth q], QA [auth r], RA [auth s], SA [auth t], TA [auth u], UA [auth v], VA [auth w], WA [auth x], XA [auth y], YA [auth z], ZA [auth 0]	L-PEPTIDE LINKING	C4 H9 N O3		THR
MP8	AB [auth 1], BB [auth 2], CA [auth c], CB [auth 3], DA [auth e], DB [auth 4], EA [auth f], FA [auth g], GA [auth h], HA [auth i], IA [auth j], JA [auth k], KA [auth l], LA [auth m], MA [auth n], NA [auth o], OA [auth p], PA [auth q], QA [auth r], RA [auth s], SA [auth t], TA [auth u], UA [auth v], VA [auth w], WA [auth x], XA [auth y], YA [auth z], ZA [auth 0]	L-PEPTIDE LINKING	C6 H11 N O2		PRO
WFP	AB [auth 1], BB [auth 2], CA [auth c], CB [auth 3], DA [auth e], DB [auth 4], EA [auth f], FA [auth g], GA [auth h], HA [auth i], IA [auth j], JA [auth k], KA [auth l], LA [auth m], MA [auth n], NA [auth o], OA [auth p], PA [auth q], QA [auth r], RA [auth s], SA [auth t], TA [auth u], UA [auth v], VA [auth w], WA [auth x], XA [auth y], YA [auth z], ZA [auth 0]	L-PEPTIDE LINKING	C9 H9 F2 N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.248 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.238	α = 90
b = 195.976	β = 97.42
c = 139.894	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-13 
Deposition Author(s): Mabanglo, M.F., Houry, W.A.

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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  

• 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 2.0: 2023-02-22
  Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 2.2: 2023-11-15
  Changes: Data collection