7D8E

Crystal Structure of double mutant Y115E Y117E human Secretory Glutaminyl Cyclase in complex with LSB-09

PDB DOI: https://doi.org/10.2210/pdb7D8E/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2020-10-08 Released: 2021-12-08
Deposition Author(s): Dileep, K.V., Ihara, K., Sakai, N., Shirozu, M., Zhang, K.Y.J.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.252
R-Value Work: 0.209
R-Value Observed: 0.211

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of double mutant Y115E Y117E human Secretory Glutaminyl Cyclase in complex with LSB-09

Dileep, K.V., Ihara, K., Sakai, N., Shirozu, M., Zhang, K.Y.J.

To be published.

Macromolecule Content

Total Structure Weight: 114.82 kDa
Atom Count: 8,075
Modelled Residue Count: 954
Deposited Residue Count: 987
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutaminyl-peptide cyclotransferase	A, B, C	329	Homo sapiens	Mutation(s): 2 Gene Names: QPCT EC: 2.3.2.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q16769 (Homo sapiens) Explore Q16769 Go to UniProtKB: Q16769
PHAROS: Q16769 GTEx: ENSG00000115828
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q16769
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GYO (Subject of Investigation/LOI) Query on GYO Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain Y [auth C] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain Y [auth C]	L [auth A], S [auth B], Y [auth C]	~{N}-[(1~{S},2~{S})-2-(2-methoxyphenyl)cyclopropyl]-3~{H}-benzimidazole-5-carboxamide C₁₈ H₁₇ N₃ O₂ ZKYVGLRMGWYWNE-ZFWWWQNUSA-N		Interactions Focus chain L [auth A] Focus chain S [auth B] Focus chain Y [auth C] Interactions & Density Focus chain L [auth A] Focus chain S [auth B] Focus chain Y [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	I [auth A] J [auth A] K [auth A] Q [auth B] R [auth B] I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B], W [auth C], X [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain M [auth B] SDF format, chain T [auth C] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] mmCIF format, chain D [auth A] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C]	D [auth A], M [auth B], T [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain M [auth B] Focus chain T [auth C] Interactions & Density Focus chain D [auth A] Focus chain M [auth B] Focus chain T [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File 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 N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] 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 N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] 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 N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C]	E [auth A] F [auth A] G [auth A] H [auth A] N [auth B] E [auth A], F [auth A], G [auth A], H [auth A], N [auth B], O [auth B], P [auth B], U [auth C], V [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C]