6NAH | pdb_00006nah

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.248 (Depositor), 0.251 (DCC)
R-Value Work:
0.192 (Depositor), 0.196 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.2 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: 706.94 kDa
Atom Count: 40,076
Modeled Residue Count: 5,007
Deposited Residue Count: 6,244
Unique protein chains: 2

Macromolecules

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| 3D Structure

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 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 ATCC BAA-335 / MC58)) Explore Q9JZ38 Go to UniProtKB: Q9JZ38
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9JZ38
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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] 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	3D Interactions
OCA Query on OCA Download:Ideal Coordinates CCD File SDF format, chain AC [auth z] SDF format, chain BC [auth 0] SDF format, chain CC [auth 1] SDF format, chain DC [auth 2] SDF format, chain EB [auth c] SDF format, chain EC [auth 3] SDF format, chain FB [auth e] SDF format, chain FC [auth 4] SDF format, chain GB [auth f] SDF format, chain HB [auth g] SDF format, chain IB [auth h] SDF format, chain KB [auth j] SDF format, chain LB [auth k] SDF format, chain MB [auth l] SDF format, chain NB [auth m] SDF format, chain OB [auth n] SDF format, chain PB [auth o] SDF format, chain QB [auth p] SDF format, chain RB [auth q] SDF format, chain SB [auth r] SDF format, chain TB [auth s] SDF format, chain UB [auth t] SDF format, chain VB [auth u] SDF format, chain WB [auth v] SDF format, chain XB [auth w] SDF format, chain YB [auth x] SDF format, chain ZB [auth y] SDF format, chain JB [auth i] MOL2 format, chain AC [auth z] MOL2 format, chain BC [auth 0] MOL2 format, chain CC [auth 1] MOL2 format, chain DC [auth 2] MOL2 format, chain EB [auth c] MOL2 format, chain EC [auth 3] MOL2 format, chain FB [auth e] MOL2 format, chain FC [auth 4] MOL2 format, chain GB [auth f] MOL2 format, chain HB [auth g] MOL2 format, chain IB [auth h] MOL2 format, chain KB [auth j] MOL2 format, chain LB [auth k] MOL2 format, chain MB [auth l] MOL2 format, chain NB [auth m] MOL2 format, chain OB [auth n] MOL2 format, chain PB [auth o] MOL2 format, chain QB [auth p] MOL2 format, chain RB [auth q] MOL2 format, chain SB [auth r] MOL2 format, chain TB [auth s] MOL2 format, chain UB [auth t] MOL2 format, chain VB [auth u] MOL2 format, chain WB [auth v] MOL2 format, chain XB [auth w] MOL2 format, chain YB [auth x] MOL2 format, chain ZB [auth y] MOL2 format, chain JB [auth i] mmCIF format, chain AC [auth z] mmCIF format, chain BC [auth 0] mmCIF format, chain CC [auth 1] mmCIF format, chain DC [auth 2] mmCIF format, chain EB [auth c] mmCIF format, chain EC [auth 3] mmCIF format, chain FB [auth e] mmCIF format, chain FC [auth 4] mmCIF format, chain GB [auth f] mmCIF format, chain HB [auth g] mmCIF format, chain IB [auth h] mmCIF format, chain KB [auth j] mmCIF format, chain LB [auth k] mmCIF format, chain MB [auth l] mmCIF format, chain NB [auth m] mmCIF format, chain OB [auth n] mmCIF format, chain PB [auth o] mmCIF format, chain QB [auth p] mmCIF format, chain RB [auth q] mmCIF format, chain SB [auth r] mmCIF format, chain TB [auth s] mmCIF format, chain UB [auth t] mmCIF format, chain VB [auth u] mmCIF format, chain WB [auth v] mmCIF format, chain XB [auth w] mmCIF format, chain YB [auth x] mmCIF format, chain ZB [auth y] mmCIF format, chain JB [auth i]	AC [auth z] BC [auth 0] CC [auth 1] DC [auth 2] EB [auth c] 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		Interactions Focus chain AC [auth z] Focus chain BC [auth 0] Focus chain CC [auth 1] Focus chain DC [auth 2] Focus chain EB [auth c] Focus chain EC [auth 3] Focus chain FB [auth e] Focus chain FC [auth 4] Focus chain GB [auth f] Focus chain HB [auth g] Focus chain IB [auth h] Focus chain JB [auth i] Focus chain KB [auth j] Focus chain LB [auth k] Focus chain MB [auth l] Focus chain NB [auth m] Focus chain OB [auth n] Focus chain PB [auth o] Focus chain QB [auth p] Focus chain RB [auth q] Focus chain SB [auth r] Focus chain TB [auth s] Focus chain UB [auth t] Focus chain VB [auth u] Focus chain WB [auth v] Focus chain XB [auth w] Focus chain YB [auth x] Focus chain ZB [auth y] Interactions & Density Focus chain AC [auth z] Focus chain BC [auth 0] Focus chain CC [auth 1] Focus chain DC [auth 2] Focus chain EB [auth c] Focus chain EC [auth 3] Focus chain FB [auth e] Focus chain FC [auth 4] Focus chain GB [auth f] Focus chain HB [auth g] Focus chain IB [auth h] Focus chain JB [auth i] Focus chain KB [auth j] Focus chain LB [auth k] Focus chain MB [auth l] Focus chain NB [auth m] Focus chain OB [auth n] Focus chain PB [auth o] Focus chain QB [auth p] Focus chain RB [auth q] Focus chain SB [auth r] Focus chain TB [auth s] Focus chain UB [auth t] Focus chain VB [auth u] Focus chain WB [auth v] Focus chain XB [auth w] Focus chain YB [auth x] Focus chain ZB [auth y]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALO Query on ALO	AB [auth 1] BB [auth 2] CA [auth c] CB [auth 3] DA [auth e] 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 Query on MP8	AB [auth 1] BB [auth 2] CA [auth c] CB [auth 3] DA [auth e] 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 Query on WFP	AB [auth 1] BB [auth 2] CA [auth c] CB [auth 3] DA [auth e] 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
YCP Query on YCP	AB [auth 1] BB [auth 2] CA [auth c] CB [auth 3] DA [auth e] 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		--

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.248 (Depositor), 0.251 (DCC)
R-Value Work: 0.192 (Depositor), 0.196 (DCC)
R-Value Observed: 0.193 (Depositor)

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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-11-13

Deposition Author(s):

Mabanglo, M.F.

Houry, W.A.

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 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

6NAH | pdb_00006nah

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

Literature

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

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2