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- PDB-1aqc: X11 PTB DOMAIN-10MER PEPTIDE COMPLEX -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1aqc
TitleX11 PTB DOMAIN-10MER PEPTIDE COMPLEX
Components
  • PEPTIDE
  • X11
KeywordsCOMPLEX (PEPTIDE BINDING MODULE/PEPTIDE) / COMPLEX (PEPTIDE BINDING MODULE-PEPTIDE) / PEPTIDE BINDING MODULE / PTB DOMAIN / COMPLEX (PEPTIDE BINDING MODULE-PEPTIDE) complex
Function / homology
Function and homology information


gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / axo-dendritic transport / glutamate secretion / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / presynaptic active zone membrane / presynaptic modulation of chemical synaptic transmission / locomotory behavior / intracellular protein transport ...gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / axo-dendritic transport / glutamate secretion / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / presynaptic active zone membrane / presynaptic modulation of chemical synaptic transmission / locomotory behavior / intracellular protein transport / Schaffer collateral - CA1 synapse / multicellular organism growth / synaptic vesicle / nervous system development / amyloid-beta binding / regulation of gene expression / protein-containing complex assembly / chemical synaptic transmission / dendritic spine / in utero embryonic development / cell adhesion / perinuclear region of cytoplasm / glutamatergic synapse / Golgi apparatus / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...: / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Amyloid-beta A4 precursor protein-binding family A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.3 Å
AuthorsLee, C.-H. / Zhang, Z. / Kuriyan, J.
CitationJournal: EMBO J. / Year: 1997
Title: Sequence-specific recognition of the internalization motif of the Alzheimer's amyloid precursor protein by the X11 PTB domain.
Authors: Zhang, Z. / Lee, C.H. / Mandiyan, V. / Borg, J.P. / Margolis, B. / Schlessinger, J. / Kuriyan, J.
History
DepositionJul 28, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: X11
C: PEPTIDE
B: X11
D: PEPTIDE


Theoretical massNumber of molelcules
Total (without water)42,1354
Polymers42,1354
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-29 kcal/mol
Surface area14210 Å2
MethodPISA
2
A: X11
C: PEPTIDE

B: X11
D: PEPTIDE


Theoretical massNumber of molelcules
Total (without water)42,1354
Polymers42,1354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x+1/2,-y+1/2,-z+3/41
Buried area4630 Å2
ΔGint-29 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.400, 74.400, 157.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.339, -0.537, 0.773), (0.034, 0.827, 0.561), (-0.94, -0.164, 0.298)
Vector: 10.13, -35.2, 97.66)

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Components

#1: Protein X11


Mass: 19801.256 Da / Num. of mol.: 2 / Fragment: PTB DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q02410
#2: Protein/peptide PEPTIDE


Mass: 1266.377 Da / Num. of mol.: 2 / Source method: isolated from a natural source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.4 Mammonium sulfate1reservoir
2100 mMMES1reservoir
3100 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 97157 / % possible obs: 92.4 % / Redundancy: 3.7 % / Rsym value: 0.083 / Net I/σ(I): 18.7
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 4.7 / Rsym value: 0.229 / % possible all: 80
Reflection
*PLUS
Num. obs: 18927 / Num. measured all: 69525 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 80 % / Rmerge(I) obs: 0.229

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→6 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.303 -10 %RANDOM
Rwork0.21 ---
obs0.21 17419 69 %-
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 0 0 215 2370
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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