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- PDB-4wgi: A Single Diastereomer of a Macrolactam Core Binds Specifically to... -

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Basic information

Entry
Database: PDB / ID: 4wgi
TitleA Single Diastereomer of a Macrolactam Core Binds Specifically to Myeloid Cell Leukemia 1 (MCL1)
ComponentsMaltose-binding periplasmic protein,Induced myeloid leukemia cell differentiation protein Mcl-1
Keywordsapoptosis/inhibitor / Fusion protein / MBP / transport protein / transport protein-inhibitor complex / apoptosis-inhibitor complex
Function / homology
Function and homology information


positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / carbohydrate transmembrane transporter activity ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / response to cytokine / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / Signaling by ALK fusions and activated point mutants / outer membrane-bounded periplasmic space / channel activity / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family ...Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Chem-3M6 / FORMIC ACID / Maltose/maltodextrin-binding periplasmic protein / Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsClifton, M.C. / Fairman, J.W. / Fang, C. / D'Souza, B. / Fulroth, B. / Leed, A. / McCarren, P. / Wang, L. / Wang, Y. / Kaushik, V. ...Clifton, M.C. / Fairman, J.W. / Fang, C. / D'Souza, B. / Fulroth, B. / Leed, A. / McCarren, P. / Wang, L. / Wang, Y. / Kaushik, V. / Palmer, M. / Wei, G. / Golub, T.R. / Hubbard, B.K. / Serrano-Wu, M.H.
CitationJournal: Acs Med.Chem.Lett. / Year: 2014
Title: Single Diastereomer of a Macrolactam Core Binds Specifically to Myeloid Cell Leukemia 1 (MCL1).
Authors: Fang, C. / D'Souza, B. / Thompson, C.F. / Clifton, M.C. / Fairman, J.W. / Fulroth, B. / Leed, A. / McCarren, P. / Wang, L. / Wang, Y. / Feau, C. / Kaushik, V.K. / Palmer, M. / Wei, G. / ...Authors: Fang, C. / D'Souza, B. / Thompson, C.F. / Clifton, M.C. / Fairman, J.W. / Fulroth, B. / Leed, A. / McCarren, P. / Wang, L. / Wang, Y. / Feau, C. / Kaushik, V.K. / Palmer, M. / Wei, G. / Golub, T.R. / Hubbard, B.K. / Serrano-Wu, M.H.
History
DepositionSep 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Induced myeloid leukemia cell differentiation protein Mcl-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,80414
Polymers57,3111
Non-polymers1,49313
Water8,701483
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.300, 135.870, 37.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Maltose-binding periplasmic protein,Induced myeloid leukemia cell differentiation protein Mcl-1 / MBP / MMBP / Maltodextrin-binding protein / Bcl-2-like protein 3 / Bcl2-L-3 / Bcl-2-related protein ...MBP / MMBP / Maltodextrin-binding protein / Bcl-2-like protein 3 / Bcl2-L-3 / Bcl-2-related protein EAT/mcl1 / mcl1/EAT


Mass: 57310.883 Da / Num. of mol.: 1 / Fragment: unp residues 27-392,unp residues 173-291 / Mutation: K194A, K197A, R201A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, Z5632, ECs5017, MCL1, BCL2L3 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEY0, UniProt: Q07820
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 495 molecules

#3: Chemical ChemComp-3M6 / (2S)-2-[(2S,3R)-10-{[(4-fluorophenyl)sulfonyl]amino}-3-methyl-2-[(methyl{[4-(trifluoromethyl)phenyl]carbamoyl}amino)methyl]-6-oxo-3,4-dihydro-2H-1,5-benzoxazocin-5(6H)-yl]propanoic acid


Mass: 666.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H30F4N4O7S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.22 Å3/Da / Density % sol: 44.55 % / Description: rods
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10 MG/ML MBP-MCL1 VCID 9272, 200MM MG FORMATE, 20% PEG3350, 0.5M BRD-0611, 1MM MALTOSE, CRYOPROTECTANT 20% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 44522 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 19.76 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.07 / Χ2: 1.005 / Net I/σ(I): 16.2 / Num. measured all: 196275
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.85-1.90.7490.5082.129994328232780.62299.9
1.9-1.950.7860.42.759793312931240.48899.8
1.95-2.010.8690.3013.7910040311631090.36499.8
2.01-2.070.9030.2444.929871296729620.29399.8
2.07-2.140.9150.2175.889831289328870.2699.8
2.14-2.210.950.1857.359833285428380.2299.4
2.21-2.290.9660.1529.629991268626720.17899.5
2.29-2.390.9760.13211.4110503264326260.15399.4
2.39-2.490.9810.11713.0710416251825030.13599.4
2.49-2.620.9880.10514.6110404240523880.1299.3
2.62-2.760.9910.0917.4710711229722810.10299.3
2.76-2.930.9940.0819.3810924221122030.0999.6
2.93-3.130.9960.06723.2210960207020670.07599.9
3.13-3.380.9980.05330.2311528191119080.05899.8
3.38-3.70.9990.04338.6812005177717750.04799.9
3.7-4.140.9990.03842.5911029163316310.04199.9
4.14-4.780.9990.03245.729691144814440.03599.7
4.78-5.850.9990.03343.758457123312320.03699.9
5.85-8.270.9990.02943.0467019949940.032100
8.270.9990.02648.3835936086000.02898.7

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX(phenix.refine: 1.9_1675)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WIX

3wix


Resolution: 1.85→41.206 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2126 2167 4.87 %
Rwork0.1772 42295 -
obs0.179 44462 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.28 Å2 / Biso mean: 23.4035 Å2 / Biso min: 9.53 Å2
Refinement stepCycle: final / Resolution: 1.85→41.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3904 0 100 483 4487
Biso mean--30.12 29.69 -
Num. residues----513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044109
X-RAY DIFFRACTIONf_angle_d0.8765588
X-RAY DIFFRACTIONf_chiral_restr0.031623
X-RAY DIFFRACTIONf_plane_restr0.004721
X-RAY DIFFRACTIONf_dihedral_angle_d12.8521454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.89310.29211390.266828212960100
1.8931-1.94040.30321260.241127602886100
1.9404-1.99290.28251390.208227902929100
1.9929-2.05150.24521450.203327662911100
2.0515-2.11770.22881580.206827802938100
2.1177-2.19340.25781450.19162774291999
2.1934-2.28120.21891500.18742747289799
2.2812-2.3850.221600.17882797295799
2.385-2.51070.21521490.17712796294599
2.5107-2.6680.22451340.172797293199
2.668-2.8740.2241430.1792810295399
2.874-3.16310.19481560.176128262982100
3.1631-3.62060.18621220.161828702992100
3.6206-4.56060.19551350.147529153050100
4.5606-41.21670.1741660.165730463212100
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)
10.9301-0.75030.2010.78660.0070.3295-0.1204-0.1094-0.14730.16920.08930.16850.0067-0.07610.01650.17610.01750.0580.13780.00610.152310.244319.635252.455
22.1874-0.6205-0.00212.119-0.05561.3227-0.05880.11960.13940.1208-0.0110.03490.0032-0.0555-0.00550.1259-0.00780.00930.1135-0.00350.133325.705331.7245.8017
31.1675-0.1548-0.91112.2619-0.10061.102-0.0095-0.0147-0.0544-0.03010.05420.14790.0155-0.0823-0.00560.13270.0002-0.01940.13640.00690.11816.502457.516547.7644
42.0819-1.07270.01392.1865-0.29731.14650.01710.0489-0.0708-0.2223-0.0130.02910.0878-0.07120.03260.14020.01420.00270.13220.01020.102117.98453.513144.2115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -196 through 137 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 172 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 173 through 253 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 254 through 321 )A0

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