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3cm2

Crystal Structure of XIAP BIR3 domain in complex with a Smac-mimetic compound, Smac010

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Baculoviral IAP repeat-containing protein 4

Homo sapiens

UniProt P98170

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

Other States of the Same Protein in the Database

Monomer
1c9q 1f9x 1tfq 1tft 2ecg 2jk7 2kna 3clx 3clx 3clx 3clx 3cm2

81 assemblies; showing the first 12

Homodimer
2opy 2poi 2qra 2qra 3clx 3clx 3cm2 3cm2 3cm2 3cm2 3cm2 3cm7

35 assemblies; showing the first 12

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1g3f 1g73 1g73 1i3o 1i4o 1i4o 1i4o 1i51 1kmc 1nw9 2opz 2opz

29 assemblies; showing the first 12

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 Author chain E； PDBConstruct 15–130； UniProt 241–356 Author chain F； PDBConstruct 15–130； UniProt 241–356 Author chain G； PDBConstruct 15–130； UniProt 241–356 Author chain H； PDBConstruct 15–130； UniProt 241–356 Author chain I； PDBConstruct 15–130； UniProt 241–356 Author chain J； 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_id3cm2
Deposition date deposition_date2008-03-20
Structure title titleCrystal Structure of XIAP BIR3 domain in complex with a Smac-mimetic compound, Smac010
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 methodX-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.

3cm2__assembly_1__model_1

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

Download this curve (.dat)

3cm2__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3cm2__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）22.93 Å
Rg (electron density)22.82 Å
Total Rg23.45 Å
Atom count1744
Residues205
Excluded volume30863 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3cm2__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3cm2__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3cm2__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3cm2__assembly_4__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 3cm2__assembly_5__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 3cm2__assembly_6__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 3cm2__assembly_7__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
8 1 3cm2__assembly_8__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
9 1 3cm2__assembly_9__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
10 1 3cm2__assembly_10__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
11 1 3cm2__assembly_11__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
12 1 3cm2__assembly_12__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
13 1 3cm2__assembly_13__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
14 1 3cm2__assembly_14__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
15 1 3cm2__assembly_15__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)

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_idd3cm2a_
Class classg — Small proteins
Fold Fold foldg.52 — Inhibitor of apoptosis (IAP) repeat
Superfamily Superfamily superfamilyg.52.1 — Inhibitor of apoptosis (IAP) repeat
Family Family familyg.52.1.1 — Inhibitor of apoptosis (IAP) repeat
Domain ID domain_idd3cm2b_
Class classg — Small proteins
Fold Fold foldg.52 — Inhibitor of apoptosis (IAP) repeat
Superfamily Superfamily superfamilyg.52.1 — Inhibitor of apoptosis (IAP) repeat
Family Family familyg.52.1.1 — Inhibitor of apoptosis (IAP) repeat
Domain ID domain_idd3cm2c_
Class classg — Small proteins
Fold Fold foldg.52 — Inhibitor of apoptosis (IAP) repeat
Superfamily Superfamily superfamilyg.52.1 — Inhibitor of apoptosis (IAP) repeat
Family Family familyg.52.1.1 — Inhibitor of apoptosis (IAP) repeat
Domain ID domain_idd3cm2d_
Class classg — Small proteins
Fold Fold foldg.52 — Inhibitor of apoptosis (IAP) repeat
Superfamily Superfamily superfamilyg.52.1 — Inhibitor of apoptosis (IAP) repeat
Family Family familyg.52.1.1 — Inhibitor of apoptosis (IAP) repeat
Domain ID domain_idd3cm2e_
Class classg — Small proteins
Fold Fold foldg.52 — Inhibitor of apoptosis (IAP) repeat
Superfamily Superfamily superfamilyg.52.1 — Inhibitor of apoptosis (IAP) repeat
Family Family familyg.52.1.1 — Inhibitor of apoptosis (IAP) repeat
Domain ID domain_idd3cm2f_
Class classg — Small proteins
Fold Fold foldg.52 — Inhibitor of apoptosis (IAP) repeat
Superfamily Superfamily superfamilyg.52.1 — Inhibitor of apoptosis (IAP) repeat
Family Family familyg.52.1.1 — Inhibitor of apoptosis (IAP) repeat
Domain ID domain_idd3cm2g_
Class classg — Small proteins
Fold Fold foldg.52 — Inhibitor of apoptosis (IAP) repeat
Superfamily Superfamily superfamilyg.52.1 — Inhibitor of apoptosis (IAP) repeat
Family Family familyg.52.1.1 — Inhibitor of apoptosis (IAP) repeat
Domain ID domain_idd3cm2h_
Class classg — Small proteins
Fold Fold foldg.52 — Inhibitor of apoptosis (IAP) repeat
Superfamily Superfamily superfamilyg.52.1 — Inhibitor of apoptosis (IAP) repeat
Family Family familyg.52.1.1 — Inhibitor of apoptosis (IAP) repeat
Domain ID domain_idd3cm2i_
Class classg — Small proteins
Fold Fold foldg.52 — Inhibitor of apoptosis (IAP) repeat
Superfamily Superfamily superfamilyg.52.1 — Inhibitor of apoptosis (IAP) repeat
Family Family familyg.52.1.1 — Inhibitor of apoptosis (IAP) repeat
Domain ID domain_idd3cm2j_
Class classg — Small proteins
Fold Fold foldg.52 — Inhibitor of apoptosis (IAP) repeat
Superfamily Superfamily superfamilyg.52.1 — Inhibitor of apoptosis (IAP) repeat
Family Family familyg.52.1.1 — Inhibitor of apoptosis (IAP) repeat

CATH v4.4 (10 domains)

Domain ID domain_id3cm2A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Homologous superfamily homologous superfamily10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Domain ID domain_id3cm2B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Homologous superfamily homologous superfamily10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Domain ID domain_id3cm2C00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Homologous superfamily homologous superfamily10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Domain ID domain_id3cm2D00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Homologous superfamily homologous superfamily10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Domain ID domain_id3cm2E00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Homologous superfamily homologous superfamily10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Domain ID domain_id3cm2F00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Homologous superfamily homologous superfamily10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Domain ID domain_id3cm2G00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Homologous superfamily homologous superfamily10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Domain ID domain_id3cm2H00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Homologous superfamily homologous superfamily10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Domain ID domain_id3cm2I00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Homologous superfamily homologous superfamily10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Domain ID domain_id3cm2J00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Homologous superfamily homologous superfamily10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
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7. Citations (1)