SAXSdb — 4gsc

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

Insulin-degrading enzyme

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 methyl N-(carboxymethyl)-N-(2-phenylethyl)glycyl-L-histidinate × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 methyl N-(carboxymethyl)-N-(2-phenylethyl)glycyl-L-histidinate × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 methyl N-(carboxymethyl)-N-(2-phenylethyl)glycyl-L-histidinate × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

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 Author chain B； PDBConstruct 13–990； UniProt 42–1019

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4gsc
Deposition date deposition_date	2012-08-27
Structure title title	Structure analysis of insulin degrading enzyme with compound bdm41559 ((s)-2-[2-(carboxymethyl-phenethyl-amino)-acetylamino]-3-(1h-imidazol-4-yl)-propionic acid methyl ester)
Keywords keywords	INSULIN DEGRADING ENZYME, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4gsc__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4gsc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4gsc__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	30.34 Å
Rg (electron density)	29.19 Å
Total Rg	30.15 Å
Atom count	7847
Residues	958
Excluded volume	140280 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4gsc__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4gsc__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4gsc__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Insulin-degrading enzyme
Molecular weight formula_weight	114560.6 kDa
EC 编号 ec_number	3.4.24.56
Mutation mutation	C110L,E111Q,C171S,C178A,C257V,C414L,C573N,C590S,C789S,C812A,C819A,C904S,C966N,C974A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	15858

MHHHHHHAAGIPMNNPAIKRIGNHITKSPEDKREYRGLELANGIKVLLISDPTTDKSSAALDVHIGSLSDPPNIAGLSHFLQHMLFLGTKKYPKENEYSQFLSEHAGSSNAFTSGEHTNYYFDVSHEHLEGALDRFAQFFLSPLFDESAKDREVNAVDSEHEKNVMNDAWRLFQLEKATGNPKHPFSKFGTGNKYTLETRPNQEGIDVRQELLKFHSAYYSSNLMAVVVLGRESLDDLTNLVVKLFSEVENKNVPLPEFPEHPFQEEHLKQLYKIVPIKDIRNLYVTFPIPDLQKYYKSNPGHYLGHLIGHEGPGSLLSELKSKGWVNTLVGGQKEGARGFMFFIINVDLTEEGLLHVEDIILHMFQYIQKLRAEGPQEWVFQELKDLNAVAFRFKDKERPRGYTSKIAGILHYYPLEEVLTAEYLLEEFRPDLIEMVLDKLRPENVRVAIVSKSFEGKTDRTEEWYGTQYKQEAIPDEVIKKWQNADLNGKFKLPTKNEFIPTNFEILPLEKEATPYPALIKDTAMSKLWFKQDDKFFLPKANLNFEFFSPFAYVDPLHSNMAYLYLELLKDSLNEYAYAAELAGLSYDLQNTIYGMYLSVKGYNDKQPILLKKIIEKMATFEIDEKRFEIIKEAYMRSLNNFRAEQPHQHAMYYLRLLMTEVAWTKDELKEALDDVTLPRLKAFIPQLLSRLHIEALLHGNITKQAALGIMQMVEDTLIEHAHTKPLLPSQLVRYREVQLPDRGWFVYQQRNEVHNNSGIEIYYQTDMQSTSENMFLELFAQIISEPAFNTLRTKEQLGYIVFSGPRRANGIQGLRFIIQSEKPPHYLESRVEAFLITMEKSIEDMTEEAFQKHIQALAIRRLDKPKKLSAESAKYWGEIISQQYNFDRDNTEVAYLKTLTKEDIIKFYKEMLAVDAPRRHKVSVHVLAREMDSNPVVGEFPAQNDINLSQAPALPQPEVIQNMTEFKRGLPLFPLVKPHINFMAAKL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	methyl N-(carboxymethyl)-N-(2-phenylethyl)glycyl-L-histidinate
Molecular weight formula_weight	388.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	180

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	4gscA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	4gscA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	4gscA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	4gscA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	4gscB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	4gscB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	4gscB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	4gscB04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

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Unit-cell length a length_a	263.759 Å
Unit-cell length b length_b	263.759 Å
Unit-cell length c length_c	91.260 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.810 Å
Low-resolution limit resolution_low	49.850 Å
R factor r_factor	0.1980
R_work r_work	0.1950
R_free r_free	0.2530

Structure analysis of insulin degrading enzyme with compound bdm41559 ((s)-2-[2-(carboxymethyl-phenethyl-amino)-acetylamino]-3-(1h-imidazol-4-yl)-propionic acid methyl ester)

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

Insulin-degrading enzyme

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4gsc__assembly_1__model_1

4gsc__assembly_1__model_1 | I(q)

4gsc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Structure analysis of insulin degrading enzyme with compound bdm41559 ((s)-2-[2-(carboxymethyl-phenethyl-amino)-acetylamino]-3-(1h-imidazol-4-yl)-propionic acid methyl ester)

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

Insulin-degrading enzyme

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4gsc__assembly_1__model_1

4gsc__assembly_1__model_1 | I(q)

4gsc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)