5cyh

CYCLOPHILIN A COMPLEXED WITH DIPEPTIDE GLY-PRO

Method: X-RAY DIFFRACTION Dmax: 48.2 Å Quality: GOOD

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

CYCLOPHILIN A

Homo sapiens

UniProt P05092

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 A; UniProt 1–164 Not recorded GLY GLYCINE × 1 PRO PROLINE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.10 Å

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.

14 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CYPH_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–164; UniProt 1–164

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 5cyh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5cyh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5cyh
Deposition date deposition_date1996-02-27
Structure title titleCYCLOPHILIN A COMPLEXED WITH DIPEPTIDE GLY-PRO
Keywords keywordsCYCLOPHILIN, COMPLEX, BINDING PROTEIN FOR CYCLOSPORIN A, (ISOMERASE-DIPEPTIDE) COMPLEX, ISOMERASE; ISOMERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier15.46
Radius of gyration Rg (electron density) rg_electron14.32
Forward intensity I(0) i06267740.00
Molecular weight molecular_weight18056.0 kDa
Excluded volume excluded_volume22506 ų
Envelope volume envelope_volume23889 ų
Hydration-shell volume shell_volume13875 ų
Envelope diameter envelope_diameter48.7
Shell Rg shell_rg20.47
Envelope Rg envelope_rg14.54
Shape Rg shape_rg14.30
Total Rg total_rg15.48
Total atoms total_atoms1559
Residues n_residues164
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 dmax48.2
Rg (real space) rg_real15.33
Rg uncertainty (real space) rg_real_error0.19
I(0) (real space) i0_real6.2680e+06
I(0) uncertainty (real space) i0_real_error6.3030e+04
Rg (reciprocal space) rg_reciprocal15.34
I(0) (reciprocal space) i0_reciprocal6268000.0000
Solution quality estimate total_estimate0.8859
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.7
Skewness Skewness skewness0.041
Kurtosis Kurtosis kurtosis-0.397
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1713000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.967

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5cyha_
Class classb — All beta proteins
Fold Fold foldb.62 — Cyclophilin-like
Superfamily Superfamily superfamilyb.62.1 — Cyclophilin-like
Family Family familyb.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

CATH v4.4 (1 domains)

Domain ID domain_id5cyhA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology100 — Cyclophilin
Homologous superfamily homologous superfamily10 — Cyclophilin-like

8. Citations (1)

9. Files and Curves (10)