8PPZ | pdb_00008ppz

Co-crystal structure of FKBP12, compound 7 and the FRB fragment of mTOR

PDB DOI: https://doi.org/10.2210/pdb8PPZ/pdb

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

Deposited: 2023-07-10 Released: 2023-08-09
Deposition Author(s): Meyners, C., Deutscher, R.C.E., Hausch, F.
Funding Organization(s): German Federal Ministry for Education and Research, German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.238 (Depositor), 0.238 (DCC)
R-Value Work:
0.192 (Depositor), 0.191 (DCC)

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

Co-crystal structure of FKBP12, compound 7 and the FRB fragment of mTOR

Meyners, C., Deutscher, R.C.E., Hausch, F.

(2023) ChemRxiv

DOI: https://doi.org/10.26434/chemrxiv-2023-4vb0m

Macromolecule Content

Total Structure Weight: 24.39 kDa
Atom Count: 1,766
Modeled Residue Count: 201
Deposited Residue Count: 205
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1A	A	107	Homo sapiens	Mutation(s): 1 Gene Names: FKBP1A, FKBP1, FKBP12 EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62942 (Homo sapiens) Explore P62942 Go to UniProtKB: P62942
PHAROS: P62942 GTEx: ENSG00000088832
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62942
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase mTOR	B	98	Homo sapiens	Mutation(s): 0 Gene Names: MTOR, FRAP, FRAP1, FRAP2, RAFT1, RAPT1 EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42345 (Homo sapiens) Explore P42345 Go to UniProtKB: P42345
PHAROS: P42345 GTEx: ENSG00000198793
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42345
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0AN (Subject of Investigation/LOI) Query on 0AN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfonyl-5-[(~{E})-2-(2-chlorophenyl)ethenyl]-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one C₂₈ H₂₆ Cl₃ N₃ O₃ S LZVLUVFCVSNKDX-MGLWIZITSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]