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- PDB-2opz: AVPF bound to BIR3-XIAP -

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Basic information

Entry
Database: PDB / ID: 2opz
TitleAVPF bound to BIR3-XIAP
Components
  • AVPF (Smac homologue, N-terminal tetrapeptide)
  • Baculoviral IAP repeat-containing protein 4
Keywordsapoptosis inhibitor / Tetrapeptide / BIR3 domain of XIAP
Function / homology
Function and homology information


endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / regulation of BMP signaling pathway / copper ion homeostasis / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / protein serine/threonine kinase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway ...endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / regulation of BMP signaling pathway / copper ion homeostasis / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / protein serine/threonine kinase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / TNFR1-induced proapoptotic signaling / regulation of innate immune response / RIPK1-mediated regulated necrosis / cysteine-type endopeptidase inhibitor activity / protein K63-linked ubiquitination / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of type I interferon production / negative regulation of tumor necrosis factor-mediated signaling pathway / Regulation of PTEN localization / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of protein ubiquitination / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Regulation of necroptotic cell death / Wnt signaling pathway / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / ubiquitin protein ligase activity / regulation of cell population proliferation / regulation of inflammatory response / neuron apoptotic process / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / defense response to bacterium / DNA damage response / negative regulation of apoptotic process / nucleoplasm / identical protein binding / metal ion 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. / Baculoviral inhibition of apoptosis protein repeat ...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
E3 ubiquitin-protein ligase XIAP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWist, A.D.
CitationJournal: Bioorg.Med.Chem. / Year: 2007
Title: Structure-activity based study of the Smac-binding pocket within the BIR3 domain of XIAP.
Authors: Wist, A.D. / Gu, L. / Riedl, S.J. / Shi, Y. / McLendon, G.L.
History
DepositionJan 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 4, 2019Group: Data collection / Category: reflns
Item: _reflns.observed_criterion_sigma_F / _reflns.observed_criterion_sigma_I ..._reflns.observed_criterion_sigma_F / _reflns.observed_criterion_sigma_I / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 4
B: Baculoviral IAP repeat-containing protein 4
C: Baculoviral IAP repeat-containing protein 4
D: Baculoviral IAP repeat-containing protein 4
E: AVPF (Smac homologue, N-terminal tetrapeptide)
F: AVPF (Smac homologue, N-terminal tetrapeptide)
G: AVPF (Smac homologue, N-terminal tetrapeptide)
H: AVPF (Smac homologue, N-terminal tetrapeptide)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,40812
Polymers52,1468
Non-polymers2624
Water0
1
A: Baculoviral IAP repeat-containing protein 4
C: Baculoviral IAP repeat-containing protein 4
E: AVPF (Smac homologue, N-terminal tetrapeptide)
G: AVPF (Smac homologue, N-terminal tetrapeptide)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2046
Polymers26,0734
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-18 kcal/mol
Surface area13090 Å2
MethodPISA
2
B: Baculoviral IAP repeat-containing protein 4
D: Baculoviral IAP repeat-containing protein 4
F: AVPF (Smac homologue, N-terminal tetrapeptide)
H: AVPF (Smac homologue, N-terminal tetrapeptide)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2046
Polymers26,0734
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-15 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.367, 170.367, 170.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

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


Mass: 12604.058 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC4, API3, IAP3, XIAP / Plasmid: pCOOL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P98170
#2: Protein/peptide
AVPF (Smac homologue, N-terminal tetrapeptide)


Mass: 432.512 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 3.95 Å3/Da / Density % sol: 68.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 1.6M magnesium sulfate heptahydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 16627 / Num. obs: 15951 / % possible obs: 95.9 %
Reflection shellHighest resolution: 3 Å / % possible all: 97.2

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Processing

Software
NameClassification
PHASERphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: B-correction resolution: 6.0 - 3.0 initial B-factor correction applied to fobs : B33= 0.000 B12= 0.000 B13= 0.000 B23= 0.000 B-factor correction applied to coordinate array B: 1.667 bulk ...Details: B-correction resolution: 6.0 - 3.0 initial B-factor correction applied to fobs : B33= 0.000 B12= 0.000 B13= 0.000 B23= 0.000 B-factor correction applied to coordinate array B: 1.667 bulk solvent: density level= 0.348327 e/A^3, B-factor= 31.8814 A^2
RfactorNum. reflection% reflection
Rfree0.277 14352 -
Rwork0.231 --
obs0.231 15951 95.9 %
all-16627 -
Displacement parametersBiso mean: 1.667 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3676 0 4 0 3680
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbonds0.011326
X-RAY DIFFRACTIONangles1.78703

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