7ZAZ | pdb_00007zaz

macrocyclase OphP with ZPP

PDB DOI: https://doi.org/10.2210/pdb7ZAZ/pdb

Classification: HYDROLASE
Organism(s): Omphalotus olearius
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2022-03-23 Released: 2022-07-06
Deposition Author(s): Song, H., Naismith, J.H.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.245 (Depositor), 0.252 (DCC)
R-Value Work:
0.209 (Depositor), 0.218 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Molecular basis for the enzymatic macrocyclization of multiply backbone N-methylated peptides

Matabaro, E., Song, H., Gherlone, F., Sonderegger, L., Giltrap, A., Liver, S., Gossert, A., Kunzler, M., Naismith, J.H.

(2022) bioRxiv

DOI: https://doi.org/10.1101/2022.07.21.500988

Macromolecule Content

Total Structure Weight: 341.75 kDa
Atom Count: 24,384
Modeled Residue Count: 2,839
Deposited Residue Count: 2,980
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolyl endopeptidase	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	745	Omphalotus olearius	Mutation(s): 0

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZPR (Subject of Investigation/LOI) Query on ZPR Download:Ideal Coordinates CCD File SDF format, chain X [auth BBB] SDF format, chain KA [auth DDD] SDF format, chain GA [auth CCC] SDF format, chain E [auth AAA] MOL2 format, chain X [auth BBB] MOL2 format, chain KA [auth DDD] MOL2 format, chain GA [auth CCC] MOL2 format, chain E [auth AAA] mmCIF format, chain X [auth BBB] mmCIF format, chain KA [auth DDD] mmCIF format, chain GA [auth CCC] mmCIF format, chain E [auth AAA]	E [auth AAA], GA [auth CCC], KA [auth DDD], X [auth BBB]	N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL C₁₈ H₂₂ N₂ O₄ ORZXYSPOAVJYRU-HOTGVXAUSA-N		Interactions Focus chain E [auth AAA] Focus chain GA [auth CCC] Focus chain KA [auth DDD] Focus chain X [auth BBB] Interactions & Density Focus chain E [auth AAA] Focus chain GA [auth CCC] Focus chain KA [auth DDD] Focus chain X [auth BBB]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain RA [auth DDD] SDF format, chain OA [auth DDD] MOL2 format, chain RA [auth DDD] MOL2 format, chain OA [auth DDD] mmCIF format, chain RA [auth DDD] mmCIF format, chain OA [auth DDD]	OA [auth DDD], RA [auth DDD]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain OA [auth DDD] Focus chain RA [auth DDD] Interactions & Density Focus chain OA [auth DDD] Focus chain RA [auth DDD]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain HA [auth CCC] MOL2 format, chain HA [auth CCC] mmCIF format, chain HA [auth CCC]	HA [auth CCC]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain HA [auth CCC] Interactions & Density Focus chain HA [auth CCC]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain S [auth BBB] SDF format, chain MA [auth DDD] SDF format, chain G [auth AAA] SDF format, chain F [auth AAA] MOL2 format, chain S [auth BBB] MOL2 format, chain MA [auth DDD] MOL2 format, chain G [auth AAA] MOL2 format, chain F [auth AAA] mmCIF format, chain S [auth BBB] mmCIF format, chain MA [auth DDD] mmCIF format, chain G [auth AAA] mmCIF format, chain F [auth AAA]	F [auth AAA], G [auth AAA], MA [auth DDD], S [auth BBB]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain MA [auth DDD] Focus chain S [auth BBB] Interactions & Density Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain MA [auth DDD] Focus chain S [auth BBB]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Q [auth AAA] SDF format, chain SA [auth DDD] SDF format, chain Z [auth BBB] SDF format, chain TA [auth DDD] SDF format, chain P [auth AAA] SDF format, chain O [auth AAA] SDF format, chain JA [auth CCC] SDF format, chain IA [auth CCC] MOL2 format, chain Q [auth AAA] MOL2 format, chain SA [auth DDD] MOL2 format, chain Z [auth BBB] MOL2 format, chain TA [auth DDD] MOL2 format, chain P [auth AAA] MOL2 format, chain O [auth AAA] MOL2 format, chain JA [auth CCC] MOL2 format, chain IA [auth CCC] mmCIF format, chain Q [auth AAA] mmCIF format, chain SA [auth DDD] mmCIF format, chain Z [auth BBB] mmCIF format, chain TA [auth DDD] mmCIF format, chain P [auth AAA] mmCIF format, chain O [auth AAA] mmCIF format, chain JA [auth CCC] mmCIF format, chain IA [auth CCC]	IA [auth CCC] JA [auth CCC] O [auth AAA] P [auth AAA] Q [auth AAA] IA [auth CCC], JA [auth CCC], O [auth AAA], P [auth AAA], Q [auth AAA], SA [auth DDD], TA [auth DDD], Z [auth BBB]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain IA [auth CCC] Focus chain JA [auth CCC] Focus chain O [auth AAA] Focus chain P [auth AAA] Focus chain Q [auth AAA] Focus chain SA [auth DDD] Focus chain TA [auth DDD] Focus chain Z [auth BBB] Interactions & Density Focus chain IA [auth CCC] Focus chain JA [auth CCC] Focus chain O [auth AAA] Focus chain P [auth AAA] Focus chain Q [auth AAA] Focus chain SA [auth DDD] Focus chain TA [auth DDD] Focus chain Z [auth BBB]
BCT Query on BCT Download:Ideal Coordinates CCD File SDF format, chain DA [auth CCC] SDF format, chain EA [auth CCC] SDF format, chain I [auth AAA] SDF format, chain LA [auth DDD] SDF format, chain R [auth BBB] SDF format, chain Y [auth BBB] SDF format, chain W [auth BBB] SDF format, chain V [auth BBB] SDF format, chain UA [auth DDD] SDF format, chain U [auth BBB] SDF format, chain T [auth BBB] SDF format, chain QA [auth DDD] SDF format, chain PA [auth DDD] SDF format, chain NA [auth DDD] SDF format, chain N [auth AAA] SDF format, chain M [auth AAA] SDF format, chain L [auth AAA] SDF format, chain K [auth AAA] SDF format, chain J [auth AAA] SDF format, chain H [auth AAA] SDF format, chain FA [auth CCC] SDF format, chain CA [auth CCC] SDF format, chain BA [auth CCC] SDF format, chain AA [auth BBB] MOL2 format, chain DA [auth CCC] MOL2 format, chain EA [auth CCC] MOL2 format, chain I [auth AAA] MOL2 format, chain LA [auth DDD] MOL2 format, chain R [auth BBB] MOL2 format, chain Y [auth BBB] MOL2 format, chain W [auth BBB] MOL2 format, chain V [auth BBB] MOL2 format, chain UA [auth DDD] MOL2 format, chain U [auth BBB] MOL2 format, chain T [auth BBB] MOL2 format, chain QA [auth DDD] MOL2 format, chain PA [auth DDD] MOL2 format, chain NA [auth DDD] MOL2 format, chain N [auth AAA] MOL2 format, chain M [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain FA [auth CCC] MOL2 format, chain CA [auth CCC] MOL2 format, chain BA [auth CCC] MOL2 format, chain AA [auth BBB] mmCIF format, chain DA [auth CCC] mmCIF format, chain EA [auth CCC] mmCIF format, chain I [auth AAA] mmCIF format, chain LA [auth DDD] mmCIF format, chain R [auth BBB] mmCIF format, chain Y [auth BBB] mmCIF format, chain W [auth BBB] mmCIF format, chain V [auth BBB] mmCIF format, chain UA [auth DDD] mmCIF format, chain U [auth BBB] mmCIF format, chain T [auth BBB] mmCIF format, chain QA [auth DDD] mmCIF format, chain PA [auth DDD] mmCIF format, chain NA [auth DDD] mmCIF format, chain N [auth AAA] mmCIF format, chain M [auth AAA] mmCIF format, chain L [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain FA [auth CCC] mmCIF format, chain CA [auth CCC] mmCIF format, chain BA [auth CCC] mmCIF format, chain AA [auth BBB]	AA [auth BBB] BA [auth CCC] CA [auth CCC] DA [auth CCC] EA [auth CCC] AA [auth BBB], BA [auth CCC], CA [auth CCC], DA [auth CCC], EA [auth CCC], FA [auth CCC], H [auth AAA], I [auth AAA], J [auth AAA], K [auth AAA], L [auth AAA], LA [auth DDD], M [auth AAA], N [auth AAA], NA [auth DDD], PA [auth DDD], QA [auth DDD], R [auth BBB], T [auth BBB], U [auth BBB], UA [auth DDD], V [auth BBB], W [auth BBB], Y [auth BBB]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain AA [auth BBB] Focus chain BA [auth CCC] Focus chain CA [auth CCC] Focus chain DA [auth CCC] Focus chain EA [auth CCC] Focus chain FA [auth CCC] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain LA [auth DDD] Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain NA [auth DDD] Focus chain PA [auth DDD] Focus chain QA [auth DDD] Focus chain R [auth BBB] Focus chain T [auth BBB] Focus chain U [auth BBB] Focus chain UA [auth DDD] Focus chain V [auth BBB] Focus chain W [auth BBB] Focus chain Y [auth BBB] Interactions & Density Focus chain AA [auth BBB] Focus chain BA [auth CCC] Focus chain CA [auth CCC] Focus chain DA [auth CCC] Focus chain EA [auth CCC] Focus chain FA [auth CCC] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain LA [auth DDD] Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain NA [auth DDD] Focus chain PA [auth DDD] Focus chain QA [auth DDD] Focus chain R [auth BBB] Focus chain T [auth BBB] Focus chain U [auth BBB] Focus chain UA [auth DDD] Focus chain V [auth BBB] Focus chain W [auth BBB] Focus chain Y [auth BBB]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain VA [auth DDD] MOL2 format, chain VA [auth DDD] mmCIF format, chain VA [auth DDD]	VA [auth DDD]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain VA [auth DDD] Interactions & Density Focus chain VA [auth DDD]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000692 (ZPR) Query on PRD_000692	E [auth AAA], GA [auth CCC], KA [auth DDD], X [auth BBB]	Z-PRO-PROLINAL	Peptide-like / Inhibitor		Interactions Focus chain E [auth AAA] Focus chain GA [auth CCC] Focus chain KA [auth DDD] Focus chain X [auth BBB] Interactions & Density Focus chain E [auth AAA] Focus chain GA [auth CCC] Focus chain KA [auth DDD] Focus chain X [auth BBB]