SAXSdb — 3cm7

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

Baculoviral IAP repeat-containing protein 4

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	ZINC ION × 2 ;(3S,6S,7S,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-N-(diphenylmethyl)-7-(hydroxymethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide ; × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 ;(3S,6S,7S,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-N-(diphenylmethyl)-7-(hydroxymethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide ; × 2 water × 2	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 1 ;(3S,6S,7S,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-N-(diphenylmethyl)-7-(hydroxymethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide ; × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 1 ;(3S,6S,7S,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-N-(diphenylmethyl)-7-(hydroxymethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide ; × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	ZINC ION × 1 ;(3S,6S,7S,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-N-(diphenylmethyl)-7-(hydroxymethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide ; × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	ZINC ION × 1 ;(3S,6S,7S,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-N-(diphenylmethyl)-7-(hydroxymethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide ; × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BIRC4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–130； UniProt 241–356 Author chain B； PDBConstruct 15–130； UniProt 241–356 Author chain C； PDBConstruct 15–130； UniProt 241–356 Author chain D； PDBConstruct 15–130； UniProt 241–356

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	3cm7
Deposition date deposition_date	2008-03-21
Structure title title	Crystal Structure of XIAP-BIR3 domain in complex with Smac-mimetic compuond, Smac005
Keywords keywords	;Zinc-finger, Apoptosis, Cytoplasm, Ligase, Metal-binding, Phosphoprotein, Polymorphism, Protease inhibitor, Thiol protease inhibitor, Ubl conjugation, Ubl conjugation pathway ;; Ligase, Apoptosis
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.

3cm7__assembly_1__model_1

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

Download this curve (.dat)

3cm7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cm7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.64 Å
Rg (electron density)	22.32 Å
Total Rg	23.02 Å
Atom count	1785
Residues	201
Excluded volume	31726 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cm7__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3cm7__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3cm7__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3cm7__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3cm7__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3cm7__assembly_6__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 (4)

Entity 1 Entity 1 polymer

Description description	Baculoviral IAP repeat-containing protein 4
Molecular weight formula_weight	14675.3 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,A,B,D
Atom count atom_count	3532

MASMTGGQQMGRGSSDAVSSDRNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVRTT

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	4

Entity 3 Entity 3 non-polymer

Description description	;(3S,6S,7S,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-N-(diphenylmethyl)-7-(hydroxymethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide ;
Molecular weight formula_weight	492.6 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	17

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3cm7a_
Class class	g — Small proteins
Fold Fold fold	g.52 — Inhibitor of apoptosis (IAP) repeat
Superfamily Superfamily superfamily	g.52.1 — Inhibitor of apoptosis (IAP) repeat
Family Family family	g.52.1.1 — Inhibitor of apoptosis (IAP) repeat

Domain ID domain_id	d3cm7b_
Class class	g — Small proteins
Fold Fold fold	g.52 — Inhibitor of apoptosis (IAP) repeat
Superfamily Superfamily superfamily	g.52.1 — Inhibitor of apoptosis (IAP) repeat
Family Family family	g.52.1.1 — Inhibitor of apoptosis (IAP) repeat

Domain ID domain_id	d3cm7c_
Class class	g — Small proteins
Fold Fold fold	g.52 — Inhibitor of apoptosis (IAP) repeat
Superfamily Superfamily superfamily	g.52.1 — Inhibitor of apoptosis (IAP) repeat
Family Family family	g.52.1.1 — Inhibitor of apoptosis (IAP) repeat

Domain ID domain_id	d3cm7d_
Class class	g — Small proteins
Fold Fold fold	g.52 — Inhibitor of apoptosis (IAP) repeat
Superfamily Superfamily superfamily	g.52.1 — Inhibitor of apoptosis (IAP) repeat
Family Family family	g.52.1.1 — Inhibitor of apoptosis (IAP) repeat

CATH v4.4 (4 domains)

Domain ID domain_id	3cm7A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Homologous superfamily homologous superfamily	10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A

Domain ID domain_id	3cm7B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Homologous superfamily homologous superfamily	10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A

Domain ID domain_id	3cm7C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Homologous superfamily homologous superfamily	10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A

Domain ID domain_id	3cm7D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Homologous superfamily homologous superfamily	10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A

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Unit-cell length a length_a	92.390 Å
Unit-cell length b length_b	92.390 Å
Unit-cell length c length_c	175.151 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2364
R_work r_work	0.2332
R_free r_free	0.2999

Crystal Structure of XIAP-BIR3 domain in complex with Smac-mimetic compuond, Smac005

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

Baculoviral IAP repeat-containing protein 4

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

3cm7__assembly_1__model_1

3cm7__assembly_1__model_1 | I(q)

3cm7__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

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of XIAP-BIR3 domain in complex with Smac-mimetic compuond, Smac005

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

Baculoviral IAP repeat-containing protein 4

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

3cm7__assembly_1__model_1

3cm7__assembly_1__model_1 | I(q)

3cm7__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

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)