7ZB1 | pdb_00007zb1

S580A with 18mer

PDB DOI: https://doi.org/10.2210/pdb7ZB1/pdb

Classification: LYASE
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: 2.00 Å
R-Value Free:
0.238 (Depositor), 0.245 (DCC)
R-Value Work:
0.205 (Depositor), 0.213 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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: 346.68 kDa
Atom Count: 24,127
Modeled Residue Count: 2,916
Deposited Residue Count: 3,052
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolyl endopeptidase	A, B, C, D	745	Omphalotus olearius	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
18mer	E, F, G, H	18	Omphalotus olearius	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain V [auth C] MOL2 format, chain V [auth C] mmCIF format, chain V [auth C]	V [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain V [auth C] Interactions & Density Focus chain V [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain I [auth A] SDF format, chain T [auth C] SDF format, chain W [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain T [auth C] MOL2 format, chain W [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain T [auth C] mmCIF format, chain W [auth C]	BA [auth D], I [auth A], T [auth C], W [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain I [auth A] Focus chain T [auth C] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain I [auth A] Focus chain T [auth C] Focus chain W [auth C]
BCT Query on BCT Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain U [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain U [auth C]	AA [auth D], CA [auth D], DA [auth D], U [auth C]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain U [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	EA [auth D] FA [auth D] GA [auth D] J [auth A] K [auth A] EA [auth D], FA [auth D], GA [auth D], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], X [auth C], Y [auth C], Z [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]

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: 2.00 Å
R-Value Free: 0.238 (Depositor), 0.245 (DCC)
R-Value Work: 0.205 (Depositor), 0.213 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.01	α = 115.81
b = 104.61	β = 98.87
c = 110.65	γ = 93.79

Software Package:

Software Name	Purpose
REFMAC	refinement
APEX	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

View more in-depth experimental data

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
Version 1.3: 2024-11-20
Changes: Structure summary