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- PDB-3f7g: Structure of the BIR domain from ML-IAP bound to a peptidomimetic -

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Basic information

Entry
Database: PDB / ID: 3f7g
TitleStructure of the BIR domain from ML-IAP bound to a peptidomimetic
ComponentsBaculoviral IAP repeat-containing protein 7
KeywordsAPOPTOSIS / ZINC BINDING / PEPTIDE COMPLEX / APOPTOSIS INHIBITION / PEPTIDOMIMETIC / SMALL MOLECULE / DRUG DESIGN / Metal-binding / Nucleus / Zinc-finger
Function / homology
Function and homology information


regulation of natural killer cell apoptotic process / lens development in camera-type eye / cysteine-type endopeptidase inhibitor activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of protein ubiquitination / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity ...regulation of natural killer cell apoptotic process / lens development in camera-type eye / cysteine-type endopeptidase inhibitor activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of protein ubiquitination / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / regulation of cell population proliferation / regulation of apoptotic process / protein ubiquitination / regulation of cell cycle / centrosome / apoptotic process / negative regulation of apoptotic process / Golgi apparatus / enzyme binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. ...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) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-389 / Baculoviral IAP repeat-containing protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / difference Fourier / Resolution: 2.3 Å
AuthorsFranklin, M.C. / Fairbrother, W.J. / Cohen, F.
Citation
Journal: J.Med.Chem. / Year: 2009
Title: Orally bioavailable antagonists of inhibitor of apoptosis proteins based on an azabicyclooctane scaffold
Authors: Cohen, F. / Alicke, B. / Elliott, L.O. / Flygare, J.A. / Goncharov, T. / Keteltas, S.F. / Franklin, M.C. / Frankovitz, S. / Stephan, J.P. / Tsui, V. / Vucic, D. / Wong, H. / Fairbrother, W.J.
#1: Journal: ACS Chem. Biol. / Year: 2006
Title: Design, synthesis, and biological activity of a potent Smac mimetic that sensitizes cancer cells to apoptosis by antagonizing IAPs.
Authors: Zobel, K. / Wang, L. / Varfolomeev, E. / Franklin, M.C. / Elliott, L.O. / Wallweber, H.J. / Okawa, D.C. / Flygare, J.A. / Vucic, D. / Fairbrother, W.J. / Deshayes, K.
#2: Journal: Biochem. J. / Year: 2005
Title: Engineering ML-IAP to produce an extraordinarily potent caspase-9 inhibitor: implications for Smac-dependent anti-apoptotic activity of ML-IAP.
Authors: Vucic, D. / Franklin, M.C. / Wallweber, H.J. / Das, K. / Eckelman, B.P. / Shin, H. / Elliott, L.O. / Deshayes, K. / Salvesen, G.S. / Fairbrother, W.J.
#3: Journal: Biochemistry / Year: 2003
Title: Structure and function analysis of peptide antagonists of melanoma inhibitor of apoptosis (ML-IAP)
Authors: Franklin, M.C. / Kadkhodayan, S. / Ackerly, H. / Alexandru, D. / Distefano, M.D. / Elliott, L.O. / Flygare, J.A. / Vucic, D. / Deshayes, K. / Fairbrother, W.J.
History
DepositionNov 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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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 7
B: Baculoviral IAP repeat-containing protein 7
C: Baculoviral IAP repeat-containing protein 7
D: Baculoviral IAP repeat-containing protein 7
E: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,94512
Polymers78,8275
Non-polymers1,1187
Water4,864270
1
A: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8312
Polymers15,7651
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8312
Polymers15,7651
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8312
Polymers15,7651
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1573
Polymers15,7651
Non-polymers3922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2953
Polymers15,7651
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
A: Baculoviral IAP repeat-containing protein 7
B: Baculoviral IAP repeat-containing protein 7
C: Baculoviral IAP repeat-containing protein 7
D: Baculoviral IAP repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6499
Polymers63,0614
Non-polymers5885
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.016, 84.016, 94.476
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsAuthors state that each asymmetric unit contains five biological units, each containing one molecule of ML-IAP with either a peptide or a peptidomimetic bound at the active site. Chains A-D form a (not biologically relevant) tetramer in which molecule A binds a peptide consisting of part of the N-terminal unstructured region of molecule D; molecule B similarly binds part of molecule C; molecule C binds molecule B; and molecule D binds molecule A. The biologically relevant complex is formed by ML-IAP molecule E binding the peptidomimetic (ligand 389).

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Components

#1: Protein
Baculoviral IAP repeat-containing protein 7 / Kidney inhibitor of apoptosis protein / KIAP / Melanoma inhibitor of apoptosis protein / ML-IAP / ...Kidney inhibitor of apoptosis protein / KIAP / Melanoma inhibitor of apoptosis protein / ML-IAP / Livin / RING finger protein 50


Mass: 15765.368 Da / Num. of mol.: 5 / Fragment: BIR domain, residues 63-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: also known as KIAP OR MLIAP OR LIVIN, BIRC7, KIAP, LIVIN, MLIAP, RNF50, UNQ5800/PRO19607/PRO21344
Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96CA5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Chemical ChemComp-389 / L-alanyl-L-valyl-N-(2,2-diphenylethyl)-L-prolinamide


Mass: 464.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H36N4O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: SODIUM ACETATE, PEG 300, DTT, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 19, 2002
RadiationMonochromator: Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing).
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 33128 / Num. obs: 32773 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 11.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3304 / Rsym value: 0.431 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: difference Fourier
Starting model: PDB entry 1OXN

1oxn


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.463 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20877 1589 4.9 %RANDOM
Rwork0.16714 ---
all0.17 31460 --
obs0.16916 31130 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.954 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.13 Å20 Å2
2--0.25 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 61 270 4283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214177
X-RAY DIFFRACTIONr_bond_other_d0.0010.022940
X-RAY DIFFRACTIONr_angle_refined_deg1.0651.935650
X-RAY DIFFRACTIONr_angle_other_deg1.1683.0037016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7765493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82822.266203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93915591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7571529
X-RAY DIFFRACTIONr_chiral_restr0.0630.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024703
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021003
X-RAY DIFFRACTIONr_nbd_refined0.1970.2847
X-RAY DIFFRACTIONr_nbd_other0.1890.22949
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22007
X-RAY DIFFRACTIONr_nbtor_other0.0880.21997
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0740.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1610.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.215
X-RAY DIFFRACTIONr_mcbond_it2.332.52532
X-RAY DIFFRACTIONr_mcbond_other0.4192.51008
X-RAY DIFFRACTIONr_mcangle_it3.38753942
X-RAY DIFFRACTIONr_scbond_it2.3842.51923
X-RAY DIFFRACTIONr_scangle_it3.42851708
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 115 -
Rwork0.265 2196 -
obs--97.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.2566-0.6248-2.14274.36791.04845.98490.1364-0.90190.3940.19410.1552-0.649-0.18550.7645-0.2916-0.0431-0.0783-0.04870.2277-0.14490.1201-5.965679.639613.3951
27.417-0.46920.57492.56450.3922.7330.0312-0.2818-0.43680.15110.0106-0.13590.26460.1401-0.0418-0.1827-0.0256-0.005-0.12780.0001-0.2075-33.492664.34187.6704
37.2490.6297-2.14784.05610.37155.42760.25980.27150.7268-0.15840.0485-0.1046-0.53430.128-0.3083-0.0966-0.02070.0492-0.1557-0.0196-0.1524-35.027184.386617.5573
44.4587-0.6141.89392.6348-0.14144.8969-0.0463-0.24950.3414-0.0971-0.0452-0.1839-0.33350.11530.0915-0.1920.0174-0.0113-0.0869-0.0176-0.1303-7.786169.1171-6.286
54.73610.47770.06142.5544-0.33844.6424-0.02640.2226-0.3271-0.2089-0.01060.05180.2262-0.18830.037-0.2126-0.00210.0003-0.16160.004-0.18320.042754.99480.1425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A78 - 169
2X-RAY DIFFRACTION1D71 - 77
3X-RAY DIFFRACTION1A1001
4X-RAY DIFFRACTION2B78 - 171
5X-RAY DIFFRACTION2C71 - 77
6X-RAY DIFFRACTION3C78 - 171
7X-RAY DIFFRACTION3B71 - 77
8X-RAY DIFFRACTION4D78 - 170
9X-RAY DIFFRACTION4A71 - 77
10X-RAY DIFFRACTION5E78 - 171
11X-RAY DIFFRACTION5E1 - 2

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