5oym

HIV Integrase Binding Domain of Lens Epithelium-Derived Growth Factor

Method: X-RAY DIFFRACTION D_max: 91.4 Å Quality: REASONABLE

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

PC4 and SFRS1-interacting protein

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 345–431 Chain B； UniProt 345–431 Chain C； UniProt 345–431 Chain D； UniProt 345–431 Chain E； UniProt 345–431 Chain F； UniProt 345–431 Chain G； UniProt 345–431 Chain H； UniProt 345–431	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M Sodium Fluoride, 0.1 M bis-Tris propane, pH 8.5 and 20 % w/v PEG 3350	Resolution 2.05 Å R-free 0.236

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5OYM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Z9E Solution structure of the HIV-1 integrase-binding domain in LEDGF/p75 Deposited 2005-04-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 347–471（125 aa） Fragment：sequence database residues 347-471 contains: HIV-1 integrase-binding domain (residues 347-429)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.25；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl, 50 mM Posphate buffer；Pressure ambient NMR sample composition 0.7 mM protein, 100 mM NaCl, 50 mM Phosphate buffer, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7 mM protein, 100 mM NaCl, 38 mM Na2HPO4, 12 mM NaH2PO4, 100% D2O \| 100% D2O	Resolution not provided
2B4J Structural basis for the recognition between HIV-1 integrase and LEDGF/p75 Deposited 2005-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 347–442（96 aa） Fragment：LEDGF Chain D 347–442（96 aa） Fragment：LEDGF	Not recorded	PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；295 K；PEG-3350, Na2HPO4, NaH2PO4, KH2PO4, NACL, HEPES, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.02 Å R-free 0.226
2B4J Structural basis for the recognition between HIV-1 integrase and LEDGF/p75 Deposited 2005-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 347–442（96 aa） Fragment：LEDGF Chain D 347–442（96 aa） Fragment：LEDGF	Not recorded	PO4 PHOSPHATE ION × 4 GOL GLYCEROL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；295 K；PEG-3350, Na2HPO4, NaH2PO4, KH2PO4, NACL, HEPES, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.02 Å R-free 0.226
2M16 P75/LEDGF PWWP Domain Deposited 2012-11-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–93（93 aa） Fragment：unp residues 1-93	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 0.35；Pressure ambient NMR sample composition 0.35-0.45 mM [U-99% 13C; U-99% 15N] entity, 50 mM HEPES, 150 mM sodium chloride, 2 mM beta-mercaptoethanol, 0.66 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2MSR Solution structure of LEDGF/p75 IBD in complex with MLL1 peptide (140-160) Deposited 2014-08-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 344–426（83 aa） Fragment：UNP residues 344-425	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 125；Pressure ambient NMR sample composition 0.5 mM MLL1_140, 0.5 mM [U-13C; U-15N] IBD, 25 mM HEPES, 100 mM sodium chloride, 0.05 % beta-mercaptoethanol, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2MTN Solution structure of MLL-IBD complex Deposited 2014-08-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 337–442（106 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 50 mM potassium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2N3A Solution structure of LEDGF/p75 IBD in complex with POGZ peptide (1389-1404) Deposited 2015-05-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 348–426（79 aa） Fragment：UNP residues 348-426	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 125；Pressure ambient NMR sample composition 0.5 mM peptide, 0.5 mM [U-13C; U-15N] protein, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain m 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain q 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 12 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain u 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 13 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain G 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435 Chain W 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435 Chain i 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 14 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain C 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435 Chain K 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435 Chain a 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 15 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain m 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435 Chain q 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435 Chain u 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 16 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain O 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435 Chain S 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435 Chain e 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain O 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain S 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain W 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain a 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain e 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain i 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3HPG Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces Deposited 2009-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain G 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435 Chain H 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435 Chain K 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435 Chain L 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；291 K；25-30% Jeffamine M600, 100mM Bis-Tris propane-HCl, pH6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.28 Å R-free 0.253
3HPG Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces Deposited 2009-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain I 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435 Chain J 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435 Chain K 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435 Chain L 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；291 K；25-30% Jeffamine M600, 100mM Bis-Tris propane-HCl, pH6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.28 Å R-free 0.253
3HPG Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces Deposited 2009-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain G 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435 Chain H 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435 Chain I 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435 Chain J 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；291 K；25-30% Jeffamine M600, 100mM Bis-Tris propane-HCl, pH6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.28 Å R-free 0.253
3HPH Closed tetramer of Visna virus integrase (residues 1-219) in complex with LEDGF IBD Deposited 2009-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 348–435（88 aa） Fragment：Integrase binding domain, UNP residues 348-435 Chain F 348–435（88 aa） Fragment：Integrase binding domain, UNP residues 348-435 Chain G 348–435（88 aa） Fragment：Integrase binding domain, UNP residues 348-435 Chain H 348–435（88 aa） Fragment：Integrase binding domain, UNP residues 348-435	Not recorded	ZN ZINC ION × 4 GOL GLYCEROL × 4 PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.7-0.9M (NH4)2HPO4, 2.5% Jeffamine M600,100mM Bis-Tris propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.64 Å R-free 0.253
3U88 Crystal structure of human menin in complex with MLL1 and LEDGF Deposited 2011-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 347–435（89 aa）	Not recorded	CHD CHOLIC ACID × 1 GGB L-CANAVANINE × 4 0BR (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol × 1 GLV GLYOXYLIC ACID × 4 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；277 K；1.6 M ammonium sulfate, pH 7.0, vapor diffusion, hanging drop, temperature 277K	Resolution 3.00 Å R-free 0.233
3U88 Crystal structure of human menin in complex with MLL1 and LEDGF Deposited 2011-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 347–435（89 aa）	Not recorded	CHD CHOLIC ACID × 1 GGB L-CANAVANINE × 1 0BR (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol × 1 GLV GLYOXYLIC ACID × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；277 K；1.6 M ammonium sulfate, pH 7.0, vapor diffusion, hanging drop, temperature 277K	Resolution 3.00 Å R-free 0.233
3ZEH Solution structure of the Hs. PSIP1 PWWP domain Deposited 2012-12-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–100（98 aa） Fragment：PWWP DOMAIN, RESIDUES 3-100	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1.0 NMR sample composition 90% WATER 10% D2O 20 MM NAPI PH 6 100 MM NACL	Resolution not provided
4FU6 Crystal structure of the PSIP1 PWWP domain Deposited 2012-06-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–135（135 aa） Fragment：UNP residues 1-135	Not recorded	SO4 SULFATE ION × 3 GOL GLYCEROL × 1 UNX UNKNOWN LIGAND × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；The protein sample was treated with V8 protease. 2.5M ammonium sulfate, 0.1M TRIS, pH 8.5, vapor diffusion, temperature 291K	Resolution 2.10 Å R-free 0.232
5N88 Crystal structure of antibody bound to viral protein Deposited 2017-02-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 347–424（78 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；25.0% PEG 3350, 10mM Tris pH8.5	Resolution 1.70 Å R-free 0.252
5N88 Crystal structure of antibody bound to viral protein Deposited 2017-02-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 347–425（79 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；25.0% PEG 3350, 10mM Tris pH8.5	Resolution 1.70 Å R-free 0.252
5YI9 Solution structure of the LEDGF/p75 IBD - JPO2 (aa 56-91) complex Deposited 2017-10-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 345–442（98 aa） Fragment：UNP RESIDUES 345-442,UNP RESIDUES 345-442	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure arbitrary NMR sample composition 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD- JPO2 M2, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6EMO Solution structure of the LEDGF/p75 IBD - JPO2 (aa 1-32) complex Deposited 2017-10-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 345–442（98 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure arbitrary NMR sample composition 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD-JPO2 M1, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6EMP Solution structure of the LEDGF/p75 IBD - POGZ (aa 1370-1404) complex Deposited 2017-10-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 345–442（98 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure arbitraty NMR sample composition 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD-POGZ, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6EMQ Solution structure of the LEDGF/p75 IBD - MLL1 (aa 111-160) complex Deposited 2017-10-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 345–443（99 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure arbitrary NMR sample composition 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD-MLL1, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6EMR Solution structure of the LEDGF/p75 IBD - IWS1 (aa 446-548) complex Deposited 2017-10-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 345–441（97 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure arbitrary NMR sample composition 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD-IWS1, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6S01 Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome Deposited 2019-06-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain K 1–530（530 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging	Resolution 3.20 Å
6TRJ LEDGF/p75 IBD dimer Deposited 2019-12-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 345–430（86 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M DL-Glutamic acid monohydrate; 0.1M DL-Alanine; 0.1M Glycine; 0.1M DL-Lysine monohydrochloride; 0.1M DL-Serine; 0.1 M Tris (base); BICINE pH 8.5; 20% v/v Glycerol; 10% w/v PEG 4000 (Morpheus Molecular Dimensions condition H11)	Resolution 1.30 Å R-free 0.177
6TVM LEDGF/p75 dimer (residues 345-467) Deposited 2020-01-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 345–467（123 aa） Chain B 345–467（123 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120；Pressure 1 NMR sample composition 0.5 mM [U-13C; U-15N] LEDGF, 20 mM HEPES, 100 mM sodium chloride, 1 mM TCEP, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6ZV0 TFIIS N-terminal domain (TND) from human LEDGF/p75 Deposited 2020-07-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 345–431（87 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 225；Pressure 1 NMR sample composition 0.6 mM [U-13C; U-15N] LEDGF/p75, 25 mM [U-2H] TRIS, 200 mM sodium chloride, 1 mM TCEP, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
7OUF Structure of the STLV intasome:B56 complex bound to the strand-transfer inhibitor XZ450 Deposited 2021-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: decameric	Chain C 1–325（325 aa） Chain F 1–325（325 aa）	Not recorded	ZN ZINC ION × 4 MG MAGNESIUM ION × 4 1L0 4-azanyl-~{N}-[[2,4-bis(fluoranyl)phenyl]methyl]-6-[3-(dimethylamino)-3-oxidanylidene-propyl]-1-oxidanyl-2-oxidanylidene-1,8-naphthyridine-3-carboxamide × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7OUG STLV-1 intasome:B56 in complex with the strand-transfer inhibitor raltegravir Deposited 2021-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: decameric	Chain C 1–325（325 aa） Chain F 1–325（325 aa）	Not recorded	ZN ZINC ION × 4 MG MAGNESIUM ION × 4 RLT N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1-methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl)carbonyl]amino}ethyl)-6-oxo-1,6-di hydropyrimidine-4-carboxamide × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7PEL CryoEM structure of simian T-cell lymphotropic virus intasome in complex with PP2A regulatory subunit B56 gamma Deposited 2021-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: decameric	Chain C 1–325（325 aa） Chain F 1–325（325 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.34 Å
7Z1Z MVV strand transfer complex (STC) intasome in complex with LEDGF/p75 at 3.5 A resolution Deposited 2022-02-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 24-meric	Chain Q 347–435（89 aa） Chain R 347–435（89 aa）	Not recorded	ZN ZINC ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5；310 mM NaCl, 3 mM CaCl2, 25 mM BisTris-HCl, pH 6.5. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8CBN structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Deposited 2023-01-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain K 1–530（530 aa） Chain L 1–530（530 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.34 Å
8CBQ structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Deposited 2023-01-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain K 1–530（530 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8PC5 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex Deposited 2023-06-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain K 1–530（530 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.02 Å
8PC6 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Deposited 2023-06-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain K 1–530（530 aa） Chain L 1–530（530 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å
8PEO H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex Deposited 2023-06-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain K 1–530（530 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.69 Å
8PEP H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Deposited 2023-06-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric	Chain K 1–530（530 aa） Chain L 1–530（530 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
9BW9 Tetrameric Complex of full-length HIV-1 integrase protein bound to the integrase binding domain of LEDGF/p75 Deposited 2024-05-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 347–435（89 aa） Chain F 347–435（89 aa） Chain G 347–435（89 aa） Chain H 347–435（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Cryo-EM grids were prepared by freezing using a manual plunger in cold room at 4C	Resolution 4.10 Å
9XYC Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome LEDGF+nucleosome map Q Deposited 2025-08-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain l 2–530（529 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

34 other PDB entries and 54 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PSIP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–111； UniProt 345–431 Author chain B； PDBConstruct 25–111； UniProt 345–431 Author chain C； PDBConstruct 25–111； UniProt 345–431 Author chain D； PDBConstruct 25–111； UniProt 345–431 Author chain E； PDBConstruct 25–111； UniProt 345–431 Author chain F； PDBConstruct 25–111； UniProt 345–431 Author chain G； PDBConstruct 25–111； UniProt 345–431 Author chain H； PDBConstruct 25–111； UniProt 345–431

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5oym
Deposition date deposition_date	2017-09-11
Structure title title	HIV Integrase Binding Domain of Lens Epithelium-Derived Growth Factor
Keywords keywords	Integrase binding, transciptional co-activator, domain swap, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.91 Å
Radius of gyration Rg (electron density) rg_electron	28.30 Å
Forward intensity I(0) i0	105866000.00
Molecular weight molecular_weight	80633.0 kDa
Excluded volume excluded_volume	101320 Å³
Envelope volume envelope_volume	132000 Å³
Hydration-shell volume shell_volume	38719 Å³
Envelope diameter envelope_diameter	99.5 Å
Shell Rg shell_rg	36.04 Å
Envelope Rg envelope_rg	27.58 Å
Shape Rg shape_rg	28.26 Å
Total Rg total_rg	29.18 Å
Total atoms total_atoms	5606
Residues n_residues	687
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	91.4 Å
Rg (real space) rg_real	28.73 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	1.0590e+08
I(0) uncertainty (real space) i0_real_error	1.5760e+06
Rg (reciprocal space) rg_reciprocal	28.81 Å
I(0) (reciprocal space) i0_reciprocal	105900000.0000
Solution quality estimate total_estimate	0.6872
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.5 Å
Skewness Skewness skewness	0.079
Kurtosis Kurtosis kurtosis	-0.380
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	39190000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.830; Stabil: 0.998; Sysdev: 0.156; Positv: 1.000; Valcen: 0.993; Smooth: 0.985

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d5oyma_
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.4 — HIV integrase-binding domain
Family Family family	a.48.4.1 — HIV integrase-binding domain

Domain ID domain_id	d5oymb1
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.4 — HIV integrase-binding domain
Family Family family	a.48.4.1 — HIV integrase-binding domain

Domain ID domain_id	d5oymb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5oymc_
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.4 — HIV integrase-binding domain
Family Family family	a.48.4.1 — HIV integrase-binding domain

Domain ID domain_id	d5oymd1
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.4 — HIV integrase-binding domain
Family Family family	a.48.4.1 — HIV integrase-binding domain

Domain ID domain_id	d5oymd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5oyme_
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.4 — HIV integrase-binding domain
Family Family family	a.48.4.1 — HIV integrase-binding domain

Domain ID domain_id	d5oymf1
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.4 — HIV integrase-binding domain
Family Family family	a.48.4.1 — HIV integrase-binding domain

Domain ID domain_id	d5oymf2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5oymg1
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.4 — HIV integrase-binding domain
Family Family family	a.48.4.1 — HIV integrase-binding domain

Domain ID domain_id	d5oymg2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5oymh_
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.4 — HIV integrase-binding domain
Family Family family	a.48.4.1 — HIV integrase-binding domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	71.181 Å
Unit-cell length b length_b	54.814 Å
Unit-cell length c length_c	117.996 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.23 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	14.980 Å
R factor r_factor	0.1851
R_work r_work	0.1823
R_free r_free	0.2363

Description description	PC4 and SFRS1-interacting protein
Molecular weight formula_weight	11897.7 kDa
Source method src_method	man
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,G,A,B,C,D,E,F
Atom count atom_count	6129

HIV Integrase Binding Domain of Lens Epithelium-Derived Growth Factor

1. Protein Identity and Related Structures Protein Identity & Related Structures

PC4 and SFRS1-interacting protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	445

fit	/app/data/saxs_computation/oy/5oym/5oym.fit
pddf	/app/data/pr_computation/oy/5oym/5oym.pr.out
profile	/app/data/saxs_computation/oy/5oym/5oym.dat