9qd9

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

Method: X-RAY DIFFRACTION Dmax: 71.0 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Peptidyl-prolyl cis-trans isomerase FKBP5

Homo sapiens

UniProt Q13451

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 16–140 Mutation:A19T, C103A, C107I 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 × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;16% PEG3350, 0.1 HEPES-NaOH pH 7.5, 0.2 M ammonium acetate 10% Glycol Resolution 1.74 Å R-free 0.263
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 16–140 Mutation:A19T, C103A, C107I 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 × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;16% PEG3350, 0.1 HEPES-NaOH pH 7.5, 0.2 M ammonium acetate 10% Glycol Resolution 1.74 Å R-free 0.263

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

137 other PDB entries and 202 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FKBP5_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–128; UniProt 16–140 Author chain B; PDBConstruct 4–128; UniProt 16–140

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9qd9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9qd9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9qd9
Deposition date deposition_date2025-03-06
Structure title titleThe FK1 domain of FKBP51 in complex with the macrocyclic SAFit analog 29c
Keywords keywordsInhibitor, Complex, FKBP, ISOMERASE; ISOMERASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.84
Radius of gyration Rg (electron density) rg_electron20.74
Forward intensity I(0) i011997100.00
Molecular weight molecular_weight27524.0 kDa
Excluded volume excluded_volume35035 ų
Envelope volume envelope_volume41823 ų
Hydration-shell volume shell_volume17381 ų
Envelope diameter envelope_diameter71.0
Shell Rg shell_rg26.26
Envelope Rg envelope_rg20.68
Shape Rg shape_rg20.71
Total Rg total_rg21.64
Total atoms total_atoms3882
Residues n_residues256
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax71.0
Rg (real space) rg_real21.86
Rg uncertainty (real space) rg_real_error0.43
I(0) (real space) i0_real1.2000e+07
I(0) uncertainty (real space) i0_real_error1.4980e+05
Rg (reciprocal space) rg_reciprocal21.86
I(0) (reciprocal space) i0_reciprocal12000000.0000
Solution quality estimate total_estimate0.8895
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.3
Skewness Skewness skewness0.303
Kurtosis Kurtosis kurtosis-0.571
Angular range angular_range— – 0.3650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2130000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.991

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)