SAXSdb — 6mq3

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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 homooligomer	Homooligomer	Protein 2	;{(8R,9S,10S)-9-(2',3'-dimethyl[1,1'-biphenyl]-4-yl)-6-[(1-methyl-1H-imidazol-2-yl)sulfonyl]-1,6-diazabicyclo[6.2.0]decan-10-yl}methanol ; × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2	Review required
2	Protein homooligomer	Homooligomer	Protein 2	;{(8R,9S,10S)-9-(2',3'-dimethyl[1,1'-biphenyl]-4-yl)-6-[(1-methyl-1H-imidazol-2-yl)sulfonyl]-1,6-diazabicyclo[6.2.0]decan-10-yl}methanol ; × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2	Review required

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 1–978； UniProt 42–1019 Author chain B； PDBConstruct 1–978； 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	6mq3
Deposition date deposition_date	2018-10-09
Structure title title	Structure of Cysteine-free Human Insulin-Degrading Enzyme in complex with Substrate-selective Macrocycle Inhibitor 63
Keywords keywords	Insulin, Glucagon, Diabetes, Exo-site, HYDROLASE, 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.

6mq3__assembly_1__model_1

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

Download this curve (.dat)

6mq3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6mq3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.30 Å
Rg (electron density)	44.21 Å
Total Rg	44.48 Å
Atom count	15798
Residues	1918
Excluded volume	280400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6mq3__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6mq3__assembly_2__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	Insulin-degrading enzyme
Molecular weight formula_weight	113191.0 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	15798

MNNPAIKRIGNHITKSPEDKREYRGLELANGIKVLLISDPTTDKSSAALDVHIGSLSDPPNIAGLSHFLQHMLFLGTKKYPKENEYSQFLSEHAGSSNAFTSGEHTNYYFDVSHEHLEGALDRFAQFFLSPLFDESAKDREVNAVDSEHEKNVMNDAWRLFQLEKATGNPKHPFSKFGTGNKYTLETRPNQEGIDVRQELLKFHSAYYSSNLMAVVVLGRESLDDLTNLVVKLFSEVENKNVPLPEFPEHPFQEEHLKQLYKIVPIKDIRNLYVTFPIPDLQKYYKSNPGHYLGHLIGHEGPGSLLSELKSKGWVNTLVGGQKEGARGFMFFIINVDLTEEGLLHVEDIILHMFQYIQKLRAEGPQEWVFQELKDLNAVAFRFKDKERPRGYTSKIAGILHYYPLEEVLTAEYLLEEFRPDLIEMVLDKLRPENVRVAIVSKSFEGKTDRTEEWYGTQYKQEAIPDEVIKKWQNADLNGKFKLPTKNEFIPTNFEILPLEKEATPYPALIKDTAMSKLWFKQDDKFFLPKANLNFEFFSPFAYVDPLHSNMAYLYLELLKDSLNEYAYAAELAGLSYDLQNTIYGMYLSVKGYNDKQPILLKKIIEKMATFEIDEKRFEIIKEAYMRSLNNFRAEQPHQHAMYYLRLLMTEVAWTKDELKEALDDVTLPRLKAFIPQLLSRLHIEALLHGNITKQAALGIMQMVEDTLIEHAHTKPLLPSQLVRYREVQLPDRGWFVYQQRNEVHNNSGIEIYYQTDMQSTSENMFLELFAQIISEPAFNTLRTKEQLGYIVFSGPRRANGIQGLRFIIQSEKPPHYLESRVEAFLITMEKSIEDMTEEAFQKHIQALAIRRLDKPKKLSAESAKYWGEIISQQYNFDRDNTEVAYLKTLTKEDIIKFYKEMLAVDAPRRHKVSVHVLAREMDSNPVVGEFPAQNDINLSQAPALPQPEVIQNMTEFKRGLPLFPLVKPHINFMAAKL

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	;{(8R,9S,10S)-9-(2',3'-dimethyl[1,1'-biphenyl]-4-yl)-6-[(1-methyl-1H-imidazol-2-yl)sulfonyl]-1,6-diazabicyclo[6.2.0]decan-10-yl}methanol ;
Molecular weight formula_weight	494.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	6mq3A01
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	6mq3A02
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	6mq3A03
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	6mq3A04
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	6mq3B01
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	6mq3B02
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	6mq3B03
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	6mq3B04
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	263.254 Å
Unit-cell length b length_b	263.254 Å
Unit-cell length c length_c	91.234 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	hexagonal

Resolution resolution	3.569 Å
Low-resolution limit resolution_low	65.814 Å
R factor r_factor	0.1644
R_work r_work	0.1620
R_free r_free	0.2109

Structure of Cysteine-free Human Insulin-Degrading Enzyme in complex with Substrate-selective Macrocycle Inhibitor 63

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

6mq3__assembly_1__model_1

6mq3__assembly_1__model_1 | I(q)

6mq3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (2)

Structure of Cysteine-free Human Insulin-Degrading Enzyme in complex with Substrate-selective Macrocycle Inhibitor 63

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

6mq3__assembly_1__model_1

6mq3__assembly_1__model_1 | I(q)

6mq3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (2)