PDB-9qd9: The FK1 domain of FKBP51 in complex with the macrocyclic SAFit an...

ID or keywords:

Entry

Database: PDB / ID: 9qd9

Title

The FK1 domain of FKBP51 in complex with the macrocyclic SAFit analog 29c

Components

Peptidyl-prolyl cis-trans isomerase FKBP5

Keywords

ISOMERASE / Inhibitor / Complex / FKBP

Function / homology

Function and homology information

Modulation of host responses by IFN-stimulated genes / response to alcohol / FK506 binding / MECP2 regulates neuronal receptors and channels / : / heat shock protein binding / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cocaine / response to bacterium ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.74 Å

Authors

Meyners, C. / Brudy, C. / Hausch, F.

Funding support

Germany, 2items

Citation

Journal: J.Med.Chem. / Year: 2025
Title: Linker Modification Enables Control of Key Functional Group Orientation in Macrocycles.
Authors: Brudy, C. / Ruijsenaars, E. / Meyners, C. / Sugiarto, W.O. / Achaq, H. / Spiske, M. / Buffa, V. / Springer, M. / Repity, M. / Weller, A. / Haferkamp, U. / Pless, O. / Muschong, P. / Miltner, ...

History

Deposition	Mar 6, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 3, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9qd9.cif.gz	243.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9qd9.ent.gz		Display	PDB format
PDBx/mmJSON format	9qd9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9qd9_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	9qd9_full_validation.pdf.gz	1.2 MB	Display
Data in XML	9qd9_validation.xml.gz	14.4 KB	Display
Data in CIF	9qd9_validation.cif.gz	18.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qd/9qd9 ftp://data.pdbj.org/pub/pdb/validation_reports/qd/9qd9	HTTPS FTP

-
Related structure data

Related structure data	9qd7C 9qd8C 9qdaC 9qdbC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#141 - Sep 2011 O-GlcNAc Transferase similarity (6) #230 - Feb 2019 Initiation Factor eIF4E similarity (5) #45 - Sep 2003 Estrogen Receptor similarity (1) #166 - Oct 2013 Proteasome similarity (3) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #208 - Apr 2017 Glucose Transporters similarity (1) #217 - Jan 2018 Opioid Receptors similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #245 - May 2020 Spliceosomes similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#141 - Sep 2011
O-GlcNAc Transferase
similarity (6)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (5)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#166 - Oct 2013
Proteasome
similarity (3)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#126 - Jun 2010
Epidermal Growth Factor
similarity (1)
#208 - Apr 2017
Glucose Transporters
similarity (1)
#217 - Jan 2018
Opioid Receptors
similarity (1)
#163 - Jul 2013
HIV Capsid
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)

Deposited unit

B: Peptidyl-prolyl cis-trans isomerase FKBP5

A: Peptidyl-prolyl cis-trans isomerase FKBP5

hetero molecules

29 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: Peptidyl-prolyl cis-trans isomerase FKBP5

hetero molecules

defined by author
14.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Peptidyl-prolyl cis-trans isomerase FKBP5

hetero molecules

defined by author
14.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	48.938, 48.938, 195.364
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	B-331- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 13 - 140 / Label seq-ID: 1 - 128

Dom-ID	Auth asym-ID	Label asym-ID
1	B	A
2	A	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Peptidyl-prolyl cis-trans isomerase FKBP5 / PPIase FKBP5 / 51 kDa FK506-binding protein / FKBP-51 / 54 kDa progesterone receptor-associated ...PPIase FKBP5 / 51 kDa FK506-binding protein / FKBP-51 / 54 kDa progesterone receptor-associated immunophilin / Androgen-regulated protein 6 / FF1 antigen / FK506-binding protein 5 / FKBP-5 / FKBP54 / p54 / HSP90-binding immunophilin / Rotamase Mass: 14004.026 Da / Num. of mol.: 2 / Mutation: A19T, C103A, C107I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical	ChemComp-A1I54 / (2~{S},9~{S},12~{S})-2-cyclohexyl-20,23-dimethoxy-12-methyl-11,14,18-trioxa-4-azatricyclo[17.2.2.0^{4,9}]tricosa-1(22),19(23),20-triene-3,10-dione Mass: 503.628 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₈H₄₁NO₇ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 48.99 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 16% PEG3350, 0.1 HEPES-NaOH pH 7.5, 0.2 M ammonium acetate 10% Glycol

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.1 / Wavelength: 0.9184 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 20, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9184 Å / Relative weight: 1

Reflection

Resolution: 1.74→48.84 Å / Num. obs: 29128 / % possible obs: 99.9 % / Redundancy: 10.4 % / CC_1/2: 1 / R_merge(I) obs: 0.046 / R_pim(I) all: 0.021 / R_rim(I) all: 0.051 / Χ²: 0.96 / Net I/σ(I): 18.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
9.03-48.84	8.4	0.024	49.8	277	0.999	0.011	0.027	0.67	99.1
1.74-1.77	10.3	1.467	1.4	1524	0.603	0.688	1.625	0.83	97.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.100)	refinement
autoXDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.74→42.418 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.944 / SU B: 8.256 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.126
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2632	1494	5.142 %
R_work	0.2322	27562	-
all	0.234	-	-
obs	-	29056	99.842 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 48.659 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.556 Å²	-0.278 Å²	-0 Å²
2-	-	-0.556 Å²	0 Å²
3-	-	-	1.804 Å²

Refinement step

Cycle: LAST / Resolution: 1.74→42.418 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1875	0	72	66	2013

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	1993
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1835
X-RAY DIFFRACTION	r_angle_refined_deg	1.926	1.823	2702
X-RAY DIFFRACTION	r_angle_other_deg	0.629	1.735	4275
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.053	5	254
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.519	13.571	14
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.566	10	299
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.29	10	69
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	300
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2266
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	398
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	389
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	1709
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	1027
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.092	0.2	1079
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.118	0.2	78
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.288	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.123	0.2	41
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.266	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	3.072	2.991	1022
X-RAY DIFFRACTION	r_mcbond_other	3.064	2.99	1022
X-RAY DIFFRACTION	r_mcangle_it	3.927	5.374	1274
X-RAY DIFFRACTION	r_mcangle_other	3.929	5.375	1275
X-RAY DIFFRACTION	r_scbond_it	3.536	3.097	971
X-RAY DIFFRACTION	r_scbond_other	3.534	3.096	972
X-RAY DIFFRACTION	r_scangle_it	4.693	5.605	1428
X-RAY DIFFRACTION	r_scangle_other	4.691	5.604	1429
X-RAY DIFFRACTION	r_lrange_it	6.605	29.129	2208
X-RAY DIFFRACTION	r_lrange_other	6.607	29.105	2204
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.1	0.05	3593

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	B	X-RAY DIFFRACTION	Local ncs	0.10033	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.10033	0.05008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.74-1.782	0.337	104	0.312	1949	0.313	2089	0.9	0.922	98.2767	0.311
1.782-1.831	0.344	114	0.283	1946	0.287	2061	0.912	0.94	99.9515	0.277
1.831-1.884	0.297	89	0.28	1928	0.281	2017	0.935	0.944	100	0.267
1.884-1.942	0.342	91	0.307	1822	0.308	1914	0.918	0.933	99.9478	0.289
1.942-2.005	0.294	98	0.26	1789	0.261	1887	0.937	0.953	100	0.24
2.005-2.076	0.286	91	0.256	1737	0.258	1828	0.946	0.955	100	0.236
2.076-2.154	0.314	98	0.256	1675	0.259	1773	0.922	0.953	100	0.235
2.154-2.241	0.301	62	0.253	1654	0.255	1717	0.93	0.959	99.9418	0.231
2.241-2.341	0.294	107	0.262	1533	0.264	1641	0.941	0.956	99.9391	0.241
2.341-2.455	0.248	78	0.233	1488	0.233	1566	0.954	0.967	100	0.217
2.455-2.587	0.283	66	0.229	1427	0.232	1493	0.947	0.968	100	0.222
2.587-2.743	0.334	68	0.257	1346	0.261	1414	0.929	0.958	100	0.252
2.743-2.932	0.349	57	0.253	1278	0.257	1335	0.919	0.956	100	0.255
2.932-3.165	0.284	58	0.253	1210	0.254	1268	0.945	0.959	100	0.26
3.165-3.466	0.254	76	0.256	1099	0.256	1175	0.962	0.961	100	0.271
3.466-3.872	0.224	72	0.228	1004	0.228	1076	0.973	0.972	100	0.248
3.872-4.464	0.235	69	0.18	886	0.183	956	0.964	0.98	99.8954	0.212
4.464-5.452	0.211	50	0.182	767	0.184	818	0.973	0.979	99.8778	0.22
5.452-7.648	0.369	29	0.233	625	0.238	654	0.939	0.971	100	0.276
7.648-42.418	0.226	17	0.238	399	0.237	419	0.96	0.948	99.284	0.367

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.8518	0.1978	0.0834	3.2648	-0.1751	3.901	-0.0576	-0.0676	0.4448	-0.1845	-0.0747	0.1863	-0.2237	-0.1046	0.1322	0.1622	-0.0151	0.0339	0.0619	-0.0379	0.1081	-18.3916	0.1272	-4.0852
2	5.8059	0.4858	0.4606	2.8204	-0.1193	3.2021	0.2851	0.1143	-0.5439	-0.0939	-0.1045	0.3442	0.0564	0.1817	-0.1806	0.1583	0.0767	0.017	0.0459	-0.0041	0.1368	-9.6858	-15.6514	-29.5839

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	Bp	13 - 201
2	X-RAY DIFFRACTION	2	ALL	Ap	13 - 201

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi