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- PDB-3cm2: Crystal Structure of XIAP BIR3 domain in complex with a Smac-mime... -

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Basic information

Entry
Database: PDB / ID: 3cm2
TitleCrystal Structure of XIAP BIR3 domain in complex with a Smac-mimetic compound, Smac010
ComponentsBaculoviral IAP repeat-containing protein 4
KeywordsLigase / Apoptosis / Zinc-finger / Cytoplasm / Metal-binding / Phosphoprotein / Polymorphism / Protease inhibitor / Thiol protease inhibitor / Ubl conjugation / Ubl conjugation pathway
Function / homology
Function and homology information


regulation of apoptosis involved in tissue homeostasis / positive regulation of protein linear polyubiquitination / copper ion homeostasis / regulation of BMP signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Activation of caspases through apoptosome-mediated cleavage ...regulation of apoptosis involved in tissue homeostasis / positive regulation of protein linear polyubiquitination / copper ion homeostasis / regulation of BMP signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / regulation of innate immune response / cysteine-type endopeptidase inhibitor activity / protein K63-linked ubiquitination / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon production / protein serine/threonine kinase binding / Regulation of PTEN localization / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of JNK cascade / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / Regulation of necroptotic cell death / Wnt signaling pathway / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / regulation of inflammatory response / neuron apoptotic process / regulation of apoptotic process / response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / defense response to bacterium / DNA damage response / negative regulation of apoptotic process / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / : / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. ...XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / : / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Zinc finger, C3HC4 type (RING finger) / Death-like domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-X23 / E3 ubiquitin-protein ligase XIAP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCossu, F. / Mastrangelo, E. / Milani, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Targeting the X-linked inhibitor of apoptosis protein through 4-substituted azabicyclo[5.3.0]alkane smac mimetics. Structure, activity, and recognition principles.
Authors: Mastrangelo, E. / Cossu, F. / Milani, M. / Sorrentino, G. / Lecis, D. / Delia, D. / Manzoni, L. / Drago, C. / Seneci, P. / Scolastico, C. / Rizzo, V. / Bolognesi, M.
History
DepositionMar 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Baculoviral IAP repeat-containing protein 4
A: Baculoviral IAP repeat-containing protein 4
B: Baculoviral IAP repeat-containing protein 4
C: Baculoviral IAP repeat-containing protein 4
E: Baculoviral IAP repeat-containing protein 4
F: Baculoviral IAP repeat-containing protein 4
G: Baculoviral IAP repeat-containing protein 4
H: Baculoviral IAP repeat-containing protein 4
I: Baculoviral IAP repeat-containing protein 4
J: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,32430
Polymers146,75310
Non-polymers5,57020
Water4,288238
1
D: Baculoviral IAP repeat-containing protein 4
hetero molecules

F: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4656
Polymers29,3512
Non-polymers1,1144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
Buried area1000 Å2
ΔGint-10.1 kcal/mol
Surface area12460 Å2
MethodPISA
2
A: Baculoviral IAP repeat-containing protein 4
hetero molecules

J: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4656
Polymers29,3512
Non-polymers1,1144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_446x-1/2,-y-1/2,-z+11
Buried area970 Å2
ΔGint-11.7 kcal/mol
Surface area12600 Å2
MethodPISA
3
B: Baculoviral IAP repeat-containing protein 4
H: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4656
Polymers29,3512
Non-polymers1,1144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-8.8 kcal/mol
Surface area12430 Å2
MethodPISA
4
C: Baculoviral IAP repeat-containing protein 4
I: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4656
Polymers29,3512
Non-polymers1,1144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-11.1 kcal/mol
Surface area12470 Å2
MethodPISA
5
E: Baculoviral IAP repeat-containing protein 4
G: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4656
Polymers29,3512
Non-polymers1,1144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-11.3 kcal/mol
Surface area12480 Å2
MethodPISA
6
A: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2323
Polymers14,6751
Non-polymers5572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
B: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2323
Polymers14,6751
Non-polymers5572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
C: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2323
Polymers14,6751
Non-polymers5572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
D: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2323
Polymers14,6751
Non-polymers5572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
E: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2323
Polymers14,6751
Non-polymers5572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
F: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2323
Polymers14,6751
Non-polymers5572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
G: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2323
Polymers14,6751
Non-polymers5572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
H: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2323
Polymers14,6751
Non-polymers5572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
I: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2323
Polymers14,6751
Non-polymers5572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
J: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2323
Polymers14,6751
Non-polymers5572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.529, 108.349, 225.308
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Baculoviral IAP repeat-containing protein 4 / E3 ubiquitin-protein ligase XIAP / Inhibitor of apoptosis protein 3 / X- linked inhibitor of ...E3 ubiquitin-protein ligase XIAP / Inhibitor of apoptosis protein 3 / X- linked inhibitor of apoptosis protein / X-linked IAP / IAP-like protein / HILP


Mass: 14675.340 Da / Num. of mol.: 10 / Fragment: UNP residues 241-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC4, API3, IAP3, XIAP / Production host: Escherichia coli (E. coli)
References: UniProt: P98170, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-X23 / (3S,6S,7R,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-7-(aminomethyl)-N-(diphenylmethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide / 2(S),3(S),6(S),7(S),9a(S) 6-(2-Amino-butyrylamino)-7-aminomethyl-5-oxo-octahydro-pyrrolo[1,2-a]azepine-3-carboxylic acid benzhydryl-amide


Mass: 491.625 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C28H37N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 12% PEG 10K, 10% glycerol, 0.1M NaCl, pH 8.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 14, 2007
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 66532 / Num. obs: 66464 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 14
Reflection shellHighest resolution: 2.5 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CLX

3clx


Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.322 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26379 3376 5.1 %RANDOM
Rwork0.22085 ---
all0.22306 ---
obs0.22306 63088 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.255 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----3.4 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8344 0 370 238 8952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0218998
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.96612210
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40551014
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73824.091440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.312151394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0031540
X-RAY DIFFRACTIONr_chiral_restr0.210.21215
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027036
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.24152
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.26035
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.010.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.2107
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.72225120
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.16638193
X-RAY DIFFRACTIONr_scbond_it4.07143878
X-RAY DIFFRACTIONr_scangle_it6.16664017
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 248 -
Rwork0.274 4585 -
obs--100 %

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