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Basic information

Entry
Database: PDB / ID: 4owi
Titlepeptide structure
Componentsp53LZ2
KeywordsUNKNOWN FUNCTION / inhibitor
Function / homology
Function and homology information


protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain
Similarity search - Domain/homology
General control transcription factor GCN4
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.202 Å
AuthorsLee, J.-H.
CitationJournal: Nat Commun / Year: 2014
Title: Protein grafting of p53TAD onto a leucine zipper scaffold generates a potent HDM dual inhibitor.
Authors: Lee, J.H. / Kang, E. / Lee, J. / Kim, J. / Lee, K.H. / Han, J. / Kang, H.Y. / Ahn, S. / Oh, Y. / Shin, D. / Hur, K. / Chae, S.Y. / Song, P.H. / Kim, Y.I. / Park, J.C. / Lee, J.I.
History
DepositionFeb 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / refine_hist / struct_keywords / symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _struct_keywords.text / _symmetry.Int_Tables_number

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: p53LZ2
B: p53LZ2


Theoretical massNumber of molelcules
Total (without water)7,8612
Polymers7,8612
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-22 kcal/mol
Surface area5410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.480, 29.390, 32.700
Angle α, β, γ (deg.)90.00, 98.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide p53LZ2


Mass: 3930.679 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: P03069*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.29 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / Details: ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.2→30.165 Å / Num. obs: 17562 / % possible obs: 97.5 % / Redundancy: 6.7 % / Net I/σ(I): 59.73

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.1_743) / Classification: refinement
RefinementResolution: 1.202→30.165 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 17.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1947 879 5.01 %
Rwork0.1616 --
obs0.1632 17557 97.51 %
Solvent computationShrinkage radii: 0.05 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.185 Å2 / ksol: 0.6 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.7806 Å20 Å20.115 Å2
2--2.8368 Å20 Å2
3----1.0561 Å2
Refinement stepCycle: LAST / Resolution: 1.202→30.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms548 0 0 126 674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011554
X-RAY DIFFRACTIONf_angle_d1.157736
X-RAY DIFFRACTIONf_dihedral_angle_d10.857218
X-RAY DIFFRACTIONf_chiral_restr0.05482
X-RAY DIFFRACTIONf_plane_restr0.00788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2024-1.27780.20921410.16812679X-RAY DIFFRACTION95
1.2778-1.37640.18971490.15552827X-RAY DIFFRACTION100
1.3764-1.51490.19261500.15422835X-RAY DIFFRACTION100
1.5149-1.73410.21031490.15042830X-RAY DIFFRACTION100
1.7341-2.18470.16121510.15242866X-RAY DIFFRACTION100
2.1847-30.17420.21041390.17612641X-RAY DIFFRACTION91
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)
16.88571.5611-3.9440.9609-0.14715.3027-0.03150.0851-0.07690.05070.0013-0.0548-0.05150.06970.01890.04970.0066-0.00650.03440.00360.033413.84712.0153-6.929
28.1369-1.7387-0.23075.0735-2.66697.32820.16210.0610.1116-0.0312-0.1370.0492-0.35010.2085-0.05110.0517-0.00690.00270.03810.00270.02496.12630.34981.7057
35.4676-2.76090.67275.0526-2.38173.72040.0720.06820.1987-0.0545-0.00610.002-0.03580.0383-0.06050.0297-0.01170.00110.02220.00930.04170.8706-1.64776.1812
45.7699-1.2393-3.2691.8688-1.4648.5225-0.0634-0.06960.0627-0.003-0.00110.0536-0.0874-0.03830.08220.0377-0.0098-0.00360.02970.00020.0575-4.851-2.609210.3078
54.85862.9032-3.29087.20430.14965.6097-0.32840.1397-0.1724-0.21160.0651-0.2520.2451-0.08170.1340.0287-0.00150.00190.0696-0.00980.0473-11.9809-3.151514.2215
64.5178-2.2425-1.18084.6554-0.22514.05390.02680.07250.046-0.05590.0290.0856-0.1392-0.0493-0.06530.0386-0.01020.00270.0333-0.01060.025710.7791-2.3266-15.3402
78.21480.8223-4.3870.91550.28915.6475-0.02030.4299-0.2204-0.00320.00250.01670.1022-0.2689-0.01740.04710.007-0.00330.0503-0.01420.0524.04020.3671-10.8373
88.0837-0.4608-3.41521.50430.59083.228-0.0814-0.0723-0.26390.05110.00580.02510.05410.00890.04450.05520.00750.00660.03570.00510.0409-1.45562.2659-4.1885
94.1439-2.2307-2.95357.7134-0.56793.59210.0771-0.0573-0.02670.0665-0.13660.0918-0.07090.05210.05140.06190.0058-0.00330.0287-0.00620.0227-6.50894.7092-0.2215
107.5778-1.8790.6935.3564-0.84557.80940.09280.0763-0.0753-0.6282-0.13250.25420.0351-0.3705-0.04420.1267-0.00770.0110.065-0.00010.025-10.70334.75615.225
113.41191.4266-3.91165.0770.49965.50250.1486-0.08110.2007-0.25130.03640.0272-0.45340.3811-0.10540.0723-0.01750.02160.1137-0.01490.0434-13.51075.443512.4777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:10)
2X-RAY DIFFRACTION2(chain A and resid 11:15)
3X-RAY DIFFRACTION3(chain A and resid 16:19)
4X-RAY DIFFRACTION4(chain A and resid 20:25)
5X-RAY DIFFRACTION5(chain A and resid 26:30)
6X-RAY DIFFRACTION6(chain B and resid 1:5)
7X-RAY DIFFRACTION7(chain B and resid 6:11)
8X-RAY DIFFRACTION8(chain B and resid 12:16)
9X-RAY DIFFRACTION9(chain B and resid 17:20)
10X-RAY DIFFRACTION10(chain B and resid 21:25)
11X-RAY DIFFRACTION11(chain B and resid 26:30)

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