SAXSdb — 3e4z

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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 heterocomplex	Heteromer	Protein 2	Insulin-like growth factor II × 1 （P01344） ZINC ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Insulin-like growth factor II × 1 （P01344） ZINC ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5T5N2_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

Insulin-like growth factor II

Homo sapiens

UniProt P01344

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Insulin-degrading enzyme × 1 （Q5T5N2） ZINC ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Insulin-degrading enzyme × 1 （Q5T5N2） ZINC ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IGF2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–67； UniProt 25–91 Author chain D； PDBConstruct 1–67； UniProt 25–91

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	3e4z
Deposition date deposition_date	2008-08-12
Structure title title	Crystal structure of human insulin degrading enzyme in complex with insulin-like growth factor II
Keywords keywords	;IDE, IGF-II, DEGRADING, COMPLEX, Alternative splicing, Glycoprotein, Growth factor, Mitogen, Polymorphism, Secreted, HYDROLASE-HORMONE COMPLEX ;; HYDROLASE/HORMONE
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.

3e4z__assembly_1__model_1

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

Download this curve (.dat)

3e4z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3e4z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.17 Å
Rg (electron density)	29.03 Å
Total Rg	29.97 Å
Atom count	7846
Residues	962
Excluded volume	140330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3e4z__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3e4z__assembly_2__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	114558.7 kDa
EC 编号 ec_number	3.4.24.56
Mutation mutation	C110L, E111Q, C171S, C178A, C257V, C414L, C573N, C590S, C789S, C812A, C819A, C904S, W908Y
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	16411

MHHHHHHAAGIPMNNPAIKRIGNHITKSPEDKREYRGLELANGIKVLLISDPTTDKSSAALDVHIGSLSDPPNIAGLSHFLQHMLFLGTKKYPKENEYSQFLSEHAGSSNAFTSGEHTNYYFDVSHEHLEGALDRFAQFFLSPLFDESAKDREVNAVDSEHEKNVMNDAWRLFQLEKATGNPKHPFSKFGTGNKYTLETRPNQEGIDVRQELLKFHSAYYSSNLMAVVVLGRESLDDLTNLVVKLFSEVENKNVPLPEFPEHPFQEEHLKQLYKIVPIKDIRNLYVTFPIPDLQKYYKSNPGHYLGHLIGHEGPGSLLSELKSKGWVNTLVGGQKEGARGFMFFIINVDLTEEGLLHVEDIILHMFQYIQKLRAEGPQEWVFQELKDLNAVAFRFKDKERPRGYTSKIAGILHYYPLEEVLTAEYLLEEFRPDLIEMVLDKLRPENVRVAIVSKSFEGKTDRTEEWYGTQYKQEAIPDEVIKKWQNADLNGKFKLPTKNEFIPTNFEILPLEKEATPYPALIKDTAMSKLWFKQDDKFFLPKANLNFEFFSPFAYVDPLHSNMAYLYLELLKDSLNEYAYAAELAGLSYDLQNTIYGMYLSVKGYNDKQPILLKKIIEKMATFEIDEKRFEIIKEAYMRSLNNFRAEQPHQHAMYYLRLLMTEVAWTKDELKEALDDVTLPRLKAFIPQLLSRLHIEALLHGNITKQAALGIMQMVEDTLIEHAHTKPLLPSQLVRYREVQLPDRGWFVYQQRNEVHNNSGIEIYYQTDMQSTSENMFLELFAQIISEPAFNTLRTKEQLGYIVFSGPRRANGIQGLRFIIQSEKPPHYLESRVEAFLITMEKSIEDMTEEAFQKHIQALAIRRLDKPKKLSAESAKYYGEIISQQYNFDRDNTEVAYLKTLTKEDIIKFYKEMLAVDAPRRHKVSVHVLAREMDSCPVVGEFPCQNDINLSQAPALPQPEVIQNMTEFKRGLPLFPLVKPHINFMAAKL

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 polymer

Description description	Insulin-like growth factor II
Molecular weight formula_weight	7484.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

AYRPSETLCGGELVDTLQFVCGDRGFYFSRPASRVSRRSRGIVEECCFRSCDLALLETYCATPAKSE

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 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 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	724

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3e4zc_
Class class	g — Small proteins
Fold Fold fold	g.1 — Insulin-like
Superfamily Superfamily superfamily	g.1.1 — Insulin-like
Family Family family	g.1.1.1 — Insulin-like

Domain ID domain_id	d3e4zd_
Class class	g — Small proteins
Fold Fold fold	g.1 — Insulin-like
Superfamily Superfamily superfamily	g.1.1 — Insulin-like
Family Family family	g.1.1.1 — Insulin-like

CATH v4.4 (8 domains)

Domain ID domain_id	3e4zA01
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	3e4zA02
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	3e4zA03
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	3e4zA04
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	3e4zB01
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	3e4zB02
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	3e4zB03
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	3e4zB04
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	263.033 Å
Unit-cell length b length_b	263.033 Å
Unit-cell length c length_c	90.816 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	2.280 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1975
R_work r_work	0.1958
R_free r_free	0.2298

Crystal structure of human insulin degrading enzyme in complex with insulin-like growth factor II

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

Insulin-like growth factor II

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

3e4z__assembly_1__model_1

3e4z__assembly_1__model_1 | I(q)

3e4z__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of human insulin degrading enzyme in complex with insulin-like growth factor II

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

Insulin-like growth factor II

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

3e4z__assembly_1__model_1

3e4z__assembly_1__model_1 | I(q)

3e4z__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

CATH v4.4 (8 domains)

7. Citations (1)