7wr6

Crystal structure of ADP-riboxanated caspase-4 in complex with Af1521

Method: X-RAY DIFFRACTION Dmax: 89.2 Å Quality: GOOD

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

Caspase-4

Homo sapiens

UniProt P49662

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 102–377 Mutation:C258A ADP-ribose glycohydrolase AF_1521 × 1 (O28751) 5ZY [[(3~{a}~{S},5~{R},6~{R},6~{a}~{R})-2-azanylidene-3-[(4~{R})-4-azanyl-5-oxidanylidene-pentyl]-6-oxidanyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxazol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 9;293 K;27% PEG 3350, 0.05M CAPSO pH 9.0 Resolution 1.96 Å R-free 0.228

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.

8 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CASP4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 5–280; UniProt 102–377

ADP-ribose glycohydrolase AF_1521

Archaeoglobus fulgidus

UniProt O28751

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 B; UniProt 1–192 Not recorded Caspase-4 × 1 (P49662) 5ZY [[(3~{a}~{S},5~{R},6~{R},6~{a}~{R})-2-azanylidene-3-[(4~{R})-4-azanyl-5-oxidanylidene-pentyl]-6-oxidanyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxazol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 9;293 K;27% PEG 3350, 0.05M CAPSO pH 9.0 Resolution 1.96 Å R-free 0.228

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.

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Y1521_ARCFU
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 9–200; UniProt 1–192

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 7wr6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7wr6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7wr6
Deposition date deposition_date2022-01-26
Structure title titleCrystal structure of ADP-riboxanated caspase-4 in complex with Af1521
Keywords keywordsADP-riboxanation, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.24
Radius of gyration Rg (electron density) rg_electron26.93
Forward intensity I(0) i041937800.00
Molecular weight molecular_weight50308.0 kDa
Excluded volume excluded_volume63021 ų
Envelope volume envelope_volume76839 ų
Hydration-shell volume shell_volume25054 ų
Envelope diameter envelope_diameter94.9
Shell Rg shell_rg32.83
Envelope Rg envelope_rg26.97
Shape Rg shape_rg26.93
Total Rg total_rg27.56
Total atoms total_atoms3531
Residues n_residues441
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 dmax89.2
Rg (real space) rg_real27.44
Rg uncertainty (real space) rg_real_error0.66
I(0) (real space) i0_real4.1940e+07
I(0) uncertainty (real space) i0_real_error6.5370e+05
Rg (reciprocal space) rg_reciprocal27.38
I(0) (reciprocal space) i0_reciprocal41940000.0000
Solution quality estimate total_estimate0.8620
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.1
Skewness Skewness skewness0.480
Kurtosis Kurtosis kurtosis-0.466
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8312000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.791; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.895; Smooth: 0.933

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id7wr6A01
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)