7ZB0

macrocyclase OphP with 15mer

PDB DOI: https://doi.org/10.2210/pdb7ZB0/pdb

Classification: HYDROLASE
Organism(s): Omphalotus olearius
Expression System: Komagataella pastoris, Escherichia coli BL21(DE3)
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: 2.47 Å
R-Value Free: 0.266
R-Value Work: 0.229
R-Value Observed: 0.231

wwPDB Validation 3D Report Full Report

This is version 1.2 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: 345.01 kDa
Atom Count: 23,277
Modelled Residue Count: 2,891
Deposited Residue Count: 3,040
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolyl endopeptidase	A, B, C, D	745	Omphalotus olearius	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
15mer	E, F, G, H	15	Omphalotus olearius	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D]	M [auth C], Q [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain M [auth C] Focus chain Q [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D]	I [auth B] K [auth C] L [auth C] R [auth D] S [auth D] I [auth B], K [auth C], L [auth C], R [auth D], S [auth D], T [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D]
BCT Query on BCT Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain U [auth D] SDF format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] MOL2 format, chain W [auth D]	N [auth C] O [auth C] P [auth C] U [auth D] V [auth D] N [auth C], O [auth C], P [auth C], U [auth D], V [auth D], W [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
IML Query on IML	E, F, G, H	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		ILE
MVA Query on MVA	E, F, G, H	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL
SAR Query on SAR	E, F, G, H	PEPTIDE LINKING	C₃ H₇ N O₂		GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free: 0.266
R-Value Work: 0.229
R-Value Observed: 0.231
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.22	α = 113.04
b = 106.18	β = 101.67
c = 114.79	γ = 93.24

Software Package:

Software Name	Purpose
XDS	data reduction
xia2	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2022-07-06

Deposition Author(s):

Song, H.

Naismith, J.H.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R018189/1

Revision History (Full details and data files)

Version 1.0: 2022-07-06
Type: Initial release
Version 1.1: 2023-01-25
Changes: Database references
Version 1.2: 2024-02-07
Changes: Data collection, Derived calculations, Refinement description

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Help and Resources

7ZB0

macrocyclase OphP with 15mer

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

Entity ID: 1

Entity Groups

Sequence Annotations

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Entity ID: 2