5cjo

Crystal Structure Analysis of Elbow-Engineered-Fab-Bound Human Insulin Degrading Enzyme (IDE) in Complex with Insulin

Method: X-RAY DIFFRACTION Dmax: 145.1 Å Quality: GOOD

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

Insulin-degrading enzyme

Homo sapiens

UniProt P14735

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 42–1019 Mutation:C110L, E111Q, C171S, C178A, C257V, C414L, C573N, C590S, C789S, C812A, C819A, C904S, C966N, C974A FAB Heavy chain with engineered elbow × 2 FAB light chain × 2 Insulin × 2 (P01308) EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;291.15 K;6% v/v Tacsimate pH 7.0, 0.1 M HEPES pH 7.0, 8% w/v Polyethylene glycol monomethyl ether 5,000, and 8% v/v tert-butanol as additive. Resolution 3.29 Å R-free 0.245

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.

55 other PDB entries and 96 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IDE_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 13–990; UniProt 42–1019

Insulin

OrganismNot specified

UniProt P01308

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain a; UniProt 90–109 Not recorded Insulin-degrading enzyme × 2 (P14735) FAB Heavy chain with engineered elbow × 2 FAB light chain × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;291.15 K;6% v/v Tacsimate pH 7.0, 0.1 M HEPES pH 7.0, 8% w/v Polyethylene glycol monomethyl ether 5,000, and 8% v/v tert-butanol as additive. Resolution 3.29 Å R-free 0.245

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.

369 other PDB entries and 583 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INS_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain a; PDBConstruct 1–20; UniProt 90–109

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 5cjo

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5cjo
Deposition date deposition_date2015-07-14
Structure title titleCrystal Structure Analysis of Elbow-Engineered-Fab-Bound Human Insulin Degrading Enzyme (IDE) in Complex with Insulin
Keywords keywordsHYDROLASE, FAB, Elbow-engineer, 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_guinier41.29
Radius of gyration Rg (electron density) rg_electron41.24
Forward intensity I(0) i0349551000.00
Molecular weight molecular_weight155270.0 kDa
Excluded volume excluded_volume195520 ų
Envelope volume envelope_volume265450 ų
Hydration-shell volume shell_volume56610 ų
Envelope diameter envelope_diameter151.7
Shell Rg shell_rg43.77
Envelope Rg envelope_rg41.74
Shape Rg shape_rg41.21
Total Rg total_rg41.51
Total atoms total_atoms10966
Residues n_residues1371
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 dmax145.1
Rg (real space) rg_real41.65
Rg uncertainty (real space) rg_real_error1.64
I(0) (real space) i0_real3.4960e+08
I(0) uncertainty (real space) i0_real_error6.7740e+06
Rg (reciprocal space) rg_reciprocal41.30
I(0) (reciprocal space) i0_reciprocal349400000.0000
Solution quality estimate total_estimate0.7979
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary45.8
Skewness Skewness skewness0.661
Kurtosis Kurtosis kurtosis-0.024
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha29370000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.569; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.703

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id5cjoA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id5cjoA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id5cjoA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id5cjoA04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id5cjoH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5cjoH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5cjoL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5cjoL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)