3f7g

Structure of the BIR domain from ML-IAP bound to a peptidomimetic

Method: X-RAY DIFFRACTION Dmax: 98.1 Å Quality: GOOD

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

Baculoviral IAP repeat-containing protein 7

Homo sapiens

UniProt Q96CA5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 63–179 Fragment:BIR domain, residues 63-179 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;298 K;SODIUM ACETATE, PEG 300, DTT, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 2.30 Å R-free 0.209
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 63–179 Fragment:BIR domain, residues 63-179 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;298 K;SODIUM ACETATE, PEG 300, DTT, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 2.30 Å R-free 0.209
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 63–179 Fragment:BIR domain, residues 63-179 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;298 K;SODIUM ACETATE, PEG 300, DTT, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 2.30 Å R-free 0.209
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 63–179 Fragment:BIR domain, residues 63-179 ZN ZINC ION × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;298 K;SODIUM ACETATE, PEG 300, DTT, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 2.30 Å R-free 0.209
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain E; UniProt 63–179 Fragment:BIR domain, residues 63-179 ZN ZINC ION × 1 389 L-alanyl-L-valyl-N-(2,2-diphenylethyl)-L-prolinamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;298 K;SODIUM ACETATE, PEG 300, DTT, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 2.30 Å R-free 0.209
6 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 63–179 Chain B; UniProt 63–179 Chain C; UniProt 63–179 Chain D; UniProt 63–179 Fragment:BIR domain, residues 63-179 ZN ZINC ION × 4 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;298 K;SODIUM ACETATE, PEG 300, DTT, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 2.30 Å R-free 0.209

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

8 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BIRC7_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 24–140; UniProt 63–179 Author chain B; PDBConstruct 24–140; UniProt 63–179 Author chain C; PDBConstruct 24–140; UniProt 63–179 Author chain D; PDBConstruct 24–140; UniProt 63–179 Author chain E; PDBConstruct 24–140; UniProt 63–179

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3f7g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3f7g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3f7g
Deposition date deposition_date2008-11-09
Structure title titleStructure of the BIR domain from ML-IAP bound to a peptidomimetic
Keywords keywords;ZINC BINDING, PEPTIDE COMPLEX, APOPTOSIS INHIBITION, PEPTIDOMIMETIC, SMALL MOLECULE, DRUG DESIGN, Apoptosis, Metal-binding, Nucleus, Zinc-finger ;; APOPTOSIS
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.91
Radius of gyration Rg (electron density) rg_electron27.65
Forward intensity I(0) i053817500.00
Molecular weight molecular_weight56858.0 kDa
Excluded volume excluded_volume70667 ų
Envelope volume envelope_volume89256 ų
Hydration-shell volume shell_volume28407 ų
Envelope diameter envelope_diameter101.8
Shell Rg shell_rg33.25
Envelope Rg envelope_rg27.99
Shape Rg shape_rg27.68
Total Rg total_rg28.14
Total atoms total_atoms4013
Residues n_residues495
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax98.1
Rg (real space) rg_real28.16
Rg uncertainty (real space) rg_real_error0.94
I(0) (real space) i0_real5.3820e+07
I(0) uncertainty (real space) i0_real_error8.9450e+05
Rg (reciprocal space) rg_reciprocal28.09
I(0) (reciprocal space) i0_reciprocal53810000.0000
Solution quality estimate total_estimate0.8368
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.0
Skewness Skewness skewness0.598
Kurtosis Kurtosis kurtosis0.044
Angular range angular_range— – 0.2850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9943000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.731; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.856; Smooth: 0.825

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd3f7ga_
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_idd3f7gb_
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_idd3f7gc_
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_idd3f7gd_
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_idd3f7ge_
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 (5 domains)

Domain ID domain_id3f7gA00
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_id3f7gB00
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_id3f7gC00
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_id3f7gD00
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_id3f7gE00
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

8. Citations (4)

9. Files and Curves (10)