4ps1

Caspase-8 specific unnatural amino acid peptides

Method: X-RAY DIFFRACTION Dmax: 121.1 Å Quality: GOOD

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

Caspase-8

Homo sapiens

UniProt Q14790

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 217–479 Fragment:UNP RESIDUES 217-479 (BAL)LQ(HYP)(1U8) PEPTIDE × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;295 K;0.1 M Sodium citrate, pH 5.5, 36% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 1.73 Å R-free 0.185
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 217–479 Fragment:UNP RESIDUES 217-479 (BAL)LQ(HYP)(1U8) PEPTIDE × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;295 K;0.1 M Sodium citrate, pH 5.5, 36% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 1.73 Å R-free 0.185
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 217–479 Fragment:UNP RESIDUES 217-479 (BAL)LQ(HYP)(1U8) PEPTIDE × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;295 K;0.1 M Sodium citrate, pH 5.5, 36% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 1.73 Å R-free 0.185
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 217–479 Fragment:UNP RESIDUES 217-479 (BAL)LQ(HYP)(1U8) PEPTIDE × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;295 K;0.1 M Sodium citrate, pH 5.5, 36% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 1.73 Å R-free 0.185

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.

33 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CASP8_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–264; UniProt 217–479 Author chain B; PDBConstruct 2–264; UniProt 217–479 Author chain C; PDBConstruct 2–264; UniProt 217–479 Author chain D; PDBConstruct 2–264; UniProt 217–479

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 4ps1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ps1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4ps1
Deposition date deposition_date2014-03-06
Structure title titleCaspase-8 specific unnatural amino acid peptides
Keywords keywordsPROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier35.33
Radius of gyration Rg (electron density) rg_electron35.17
Forward intensity I(0) i0191105000.00
Molecular weight molecular_weight109780.0 kDa
Excluded volume excluded_volume136680 ų
Envelope volume envelope_volume182110 ų
Hydration-shell volume shell_volume43027 ų
Envelope diameter envelope_diameter133.8
Shell Rg shell_rg41.79
Envelope Rg envelope_rg34.70
Shape Rg shape_rg35.15
Total Rg total_rg35.70
Total atoms total_atoms7686
Residues n_residues957
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 dmax121.1
Rg (real space) rg_real35.24
Rg uncertainty (real space) rg_real_error1.12
I(0) (real space) i0_real1.9110e+08
I(0) uncertainty (real space) i0_real_error3.5010e+06
Rg (reciprocal space) rg_reciprocal35.29
I(0) (reciprocal space) i0_reciprocal191100000.0000
Solution quality estimate total_estimate0.8731
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary51.1
Skewness Skewness skewness0.170
Kurtosis Kurtosis kurtosis-0.467
Angular range angular_range— – 0.2250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha46990000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.795; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.976

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4ps1a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.17 — Caspase-like
Superfamily Superfamily superfamilyc.17.1 — Caspase-like
Family Family familyc.17.1.1 — Caspase catalytic domain
Domain ID domain_idd4ps1b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.17 — Caspase-like
Superfamily Superfamily superfamilyc.17.1 — Caspase-like
Family Family familyc.17.1.1 — Caspase catalytic domain
Domain ID domain_idd4ps1c_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.17 — Caspase-like
Superfamily Superfamily superfamilyc.17.1 — Caspase-like
Family Family familyc.17.1.1 — Caspase catalytic domain
Domain ID domain_idd4ps1d_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.17 — Caspase-like
Superfamily Superfamily superfamilyc.17.1 — Caspase-like
Family Family familyc.17.1.1 — Caspase catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id4ps1A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1460
Domain ID domain_id4ps1B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1460
Domain ID domain_id4ps1C00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1460
Domain ID domain_id4ps1D00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1460

8. Citations (1)

9. Files and Curves (10)