2i3i

Structure of an ML-IAP/XIAP chimera bound to a peptidomimetic

Method: X-RAY DIFFRACTION Dmax: 78.9 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 63–172 Fragment:ML-IAP residues 63-172 Mutation:RESIDUES 150, 160-168, AND 172 REPLACED WITH XIAP-BIR3 HOMOLOGUES ZN ZINC ION × 1 618 (3R,6R,9AR)-2,2-DIMETHYL-6-[(N-METHYL-L-ALANYL)AMINO]-N-(3-METHYL-1-PHENYL-1H-PYRAZOL-5-YL)-5-OXO-2,3,5,6,9,9A-HEXAHYDRO[1,3]THIAZOLO[3,2-A]AZEPINE-3-CARBOXAMIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;Lithium sulfate, PEG 3350, Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.30 Å R-free 0.224
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 63–172 Fragment:ML-IAP residues 63-172 Mutation:RESIDUES 150, 160-168, AND 172 REPLACED WITH XIAP-BIR3 HOMOLOGUES ZN ZINC ION × 1 618 (3R,6R,9AR)-2,2-DIMETHYL-6-[(N-METHYL-L-ALANYL)AMINO]-N-(3-METHYL-1-PHENYL-1H-PYRAZOL-5-YL)-5-OXO-2,3,5,6,9,9A-HEXAHYDRO[1,3]THIAZOLO[3,2-A]AZEPINE-3-CARBOXAMIDE × 1 LI LITHIUM ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;Lithium sulfate, PEG 3350, Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.30 Å R-free 0.224

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 51 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 24–133; UniProt 63–172 Author chain B; PDBConstruct 24–133; UniProt 63–172

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 2i3i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2i3i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2i3i
Deposition date deposition_date2006-08-18
Structure title titleStructure of an ML-IAP/XIAP chimera bound to a peptidomimetic
Keywords keywordsZINC BINDING, PEPTIDE COMPLEX, APOPTOSIS INHIBITION, PEPTIDOMIMETIC, SMALL MOLECULE, DRUG DESIGN, INHIBITOR-APOPTOSIS COMPLEX; INHIBITOR/APOPTOSIS
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.55
Radius of gyration Rg (electron density) rg_electron19.96
Forward intensity I(0) i09077280.00
Molecular weight molecular_weight22518.0 kDa
Excluded volume excluded_volume28131 ų
Envelope volume envelope_volume32191 ų
Hydration-shell volume shell_volume14794 ų
Envelope diameter envelope_diameter77.5
Shell Rg shell_rg24.82
Envelope Rg envelope_rg20.34
Shape Rg shape_rg19.92
Total Rg total_rg20.86
Total atoms total_atoms1589
Residues n_residues185
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 dmax78.9
Rg (real space) rg_real20.77
Rg uncertainty (real space) rg_real_error0.80
I(0) (real space) i0_real9.0770e+06
I(0) uncertainty (real space) i0_real_error1.2950e+05
Rg (reciprocal space) rg_reciprocal20.73
I(0) (reciprocal space) i0_reciprocal9077000.0000
Solution quality estimate total_estimate0.7552
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.3
Skewness Skewness skewness0.603
Kurtosis Kurtosis kurtosis-0.112
Angular range angular_range— – 0.3850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3135000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.478; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.385; Smooth: 0.994

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2i3ia_
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_idd2i3ib_
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 (2 domains)

Domain ID domain_id2i3iA00
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_id2i3iB00
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 (3)

9. Files and Curves (10)