7Y1X | pdb_00007y1x

Crystal structure of prolyl oligopeptidase from Microbulbifer arenaceous complex with PEG400 and MES

PDB DOI: https://doi.org/10.2210/pdb7Y1X/pdb

Classification: HYDROLASE
Organism(s): Microbulbifer arenaceous
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-06-09 Released: 2023-07-05
Deposition Author(s): Huang, P., Jiang, Z.Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free:
0.189 (Depositor), 0.190 (DCC)
R-Value Work:
0.160 (Depositor), 0.160 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of prolyl oligopeptidase from Microbulbifer arenaceous complex with PEG400 and MES

Huang, P., Jiang, Z.Q.

To be published.

Macromolecule Content

Total Structure Weight: 82 kDa
Atom Count: 6,070
Modeled Residue Count: 677
Deposited Residue Count: 711
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
prolyl oligopeptidase	A	711	Microbulbifer arenaceous	Mutation(s): 0 EC: 3.4.21.26
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
1PE (Subject of Investigation/LOI) Query on 1PE Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain D [auth A]	B [auth A], D [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain D [auth A]
MES (Subject of Investigation/LOI) Query on MES Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	C [auth A] E [auth A] F [auth A] G [auth A] H [auth A] C [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]