7ZB2 | pdb_00007zb2

apo macrocyclase OphP

PDB DOI: https://doi.org/10.2210/pdb7ZB2/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: 1.94 Å
R-Value Free:
0.241 (Depositor), 0.243 (DCC)
R-Value Work:
0.212 (Depositor), 0.212 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 677.29 kDa
Atom Count: 47,221
Modeled Residue Count: 5,755
Deposited Residue Count: 5,960
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OphP S580A	A [auth AAA] B [auth BBB] C [auth CCC] D [auth DDD] E [auth EEE] A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD], E [auth EEE], F [auth FFF], G [auth GGG], H [auth HHH]	745	Omphalotus olearius	Mutation(s): 0

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B3P Query on B3P Download:Ideal Coordinates CCD File SDF format, chain JA [auth HHH] MOL2 format, chain JA [auth HHH] mmCIF format, chain JA [auth HHH]	JA [auth HHH]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₁₁ H₂₆ N₂ O₆ HHKZCCWKTZRCCL-UHFFFAOYSA-N		Interactions Focus chain JA [auth HHH] Interactions & Density Focus chain JA [auth HHH]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain EA [auth GGG] SDF format, chain Z [auth FFF] MOL2 format, chain EA [auth GGG] MOL2 format, chain Z [auth FFF] mmCIF format, chain EA [auth GGG] mmCIF format, chain Z [auth FFF]	EA [auth GGG], Z [auth FFF]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain EA [auth GGG] Focus chain Z [auth FFF] Interactions & Density Focus chain EA [auth GGG] Focus chain Z [auth FFF]
THR Query on THR Download:Ideal Coordinates CCD File SDF format, chain S [auth EEE] SDF format, chain Y [auth FFF] MOL2 format, chain S [auth EEE] MOL2 format, chain Y [auth FFF] mmCIF format, chain S [auth EEE] mmCIF format, chain Y [auth FFF]	S [auth EEE], Y [auth FFF]	THREONINE C₄ H₉ N O₃ AYFVYJQAPQTCCC-GBXIJSLDSA-N		Interactions Focus chain S [auth EEE] Focus chain Y [auth FFF] Interactions & Density Focus chain S [auth EEE] Focus chain Y [auth FFF]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain IA [auth HHH] SDF format, chain J [auth BBB] SDF format, chain M [auth CCC] SDF format, chain P [auth DDD] SDF format, chain T [auth EEE] MOL2 format, chain IA [auth HHH] MOL2 format, chain J [auth BBB] MOL2 format, chain M [auth CCC] MOL2 format, chain P [auth DDD] MOL2 format, chain T [auth EEE] mmCIF format, chain IA [auth HHH] mmCIF format, chain J [auth BBB] mmCIF format, chain M [auth CCC] mmCIF format, chain P [auth DDD] mmCIF format, chain T [auth EEE]	IA [auth HHH], J [auth BBB], M [auth CCC], P [auth DDD], T [auth EEE]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain IA [auth HHH] Focus chain J [auth BBB] Focus chain M [auth CCC] Focus chain P [auth DDD] Focus chain T [auth EEE] Interactions & Density Focus chain IA [auth HHH] Focus chain J [auth BBB] Focus chain M [auth CCC] Focus chain P [auth DDD] Focus chain T [auth EEE]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain DA [auth GGG] SDF format, chain U [auth EEE] MOL2 format, chain DA [auth GGG] MOL2 format, chain U [auth EEE] mmCIF format, chain DA [auth GGG] mmCIF format, chain U [auth EEE]	DA [auth GGG], U [auth EEE]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth GGG] Focus chain U [auth EEE] Interactions & Density Focus chain DA [auth GGG] Focus chain U [auth EEE]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AA [auth FFF] SDF format, chain N [auth CCC] SDF format, chain O [auth CCC] MOL2 format, chain AA [auth FFF] MOL2 format, chain N [auth CCC] MOL2 format, chain O [auth CCC] mmCIF format, chain AA [auth FFF] mmCIF format, chain N [auth CCC] mmCIF format, chain O [auth CCC]	AA [auth FFF], N [auth CCC], O [auth CCC]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth FFF] Focus chain N [auth CCC] Focus chain O [auth CCC] Interactions & Density Focus chain AA [auth FFF] Focus chain N [auth CCC] Focus chain O [auth CCC]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain BA [auth FFF] SDF format, chain CA [auth FFF] SDF format, chain FA [auth GGG] SDF format, chain GA [auth GGG] SDF format, chain HA [auth GGG] SDF format, chain I [auth AAA] SDF format, chain K [auth BBB] SDF format, chain L [auth BBB] SDF format, chain Q [auth DDD] SDF format, chain R [auth DDD] SDF format, chain V [auth EEE] SDF format, chain W [auth EEE] SDF format, chain X [auth EEE] MOL2 format, chain BA [auth FFF] MOL2 format, chain CA [auth FFF] MOL2 format, chain FA [auth GGG] MOL2 format, chain GA [auth GGG] MOL2 format, chain HA [auth GGG] MOL2 format, chain I [auth AAA] MOL2 format, chain K [auth BBB] MOL2 format, chain L [auth BBB] MOL2 format, chain Q [auth DDD] MOL2 format, chain R [auth DDD] MOL2 format, chain V [auth EEE] MOL2 format, chain W [auth EEE] MOL2 format, chain X [auth EEE] mmCIF format, chain BA [auth FFF] mmCIF format, chain CA [auth FFF] mmCIF format, chain FA [auth GGG] mmCIF format, chain GA [auth GGG] mmCIF format, chain HA [auth GGG] mmCIF format, chain I [auth AAA] mmCIF format, chain K [auth BBB] mmCIF format, chain L [auth BBB] mmCIF format, chain Q [auth DDD] mmCIF format, chain R [auth DDD] mmCIF format, chain V [auth EEE] mmCIF format, chain W [auth EEE] mmCIF format, chain X [auth EEE]	BA [auth FFF] CA [auth FFF] FA [auth GGG] GA [auth GGG] HA [auth GGG] BA [auth FFF], CA [auth FFF], FA [auth GGG], GA [auth GGG], HA [auth GGG], I [auth AAA], K [auth BBB], L [auth BBB], Q [auth DDD], R [auth DDD], V [auth EEE], W [auth EEE], X [auth EEE]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth FFF] Focus chain CA [auth FFF] Focus chain FA [auth GGG] Focus chain GA [auth GGG] Focus chain HA [auth GGG] Focus chain I [auth AAA] Focus chain K [auth BBB] Focus chain L [auth BBB] Focus chain Q [auth DDD] Focus chain R [auth DDD] Focus chain V [auth EEE] Focus chain W [auth EEE] Focus chain X [auth EEE] Interactions & Density Focus chain BA [auth FFF] Focus chain CA [auth FFF] Focus chain FA [auth GGG] Focus chain GA [auth GGG] Focus chain HA [auth GGG] Focus chain I [auth AAA] Focus chain K [auth BBB] Focus chain L [auth BBB] Focus chain Q [auth DDD] Focus chain R [auth DDD] Focus chain V [auth EEE] Focus chain W [auth EEE] Focus chain X [auth EEE]