SAXSdb — 2exf

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

Nucleocapsid protein* (NC*)

OrganismNot specified

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–DNA Monomer Protein × 1 DNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 389–431	Not recorded	5'-D(GPTPCPCPCPTPGPTPTPCPGPGPGPC)-3' × 1 ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions：pH 6.5；283 K；Ionic strength (raw mmCIF value) 1mM protein, 1mM oligonucleotide；Pressure ambient NMR measurement conditions：pH 6.5；283 K；Ionic strength (raw mmCIF value) 1mM protein, 1mM oligonucleotide, 30mM NaCl, 0.2mM MgCl2；Pressure ambient NMR measurement conditions：pH 6.5；293 K；Ionic strength (raw mmCIF value) 1mM protein, 1mM oligonucleotide；Pressure ambient NMR measurement conditions：pH 6.5；293 K；Ionic strength (raw mmCIF value) 1mM protein, 1mM oligonucleotide, 30mM NaCl, 0.2mM MgCl2；Pressure ambient NMR measurement conditions：pH 6.5；303 K；Ionic strength (raw mmCIF value) 1mM protein, 1mM oligonucleotide；Pressure ambient NMR measurement conditions：pH 6.5；303 K；Ionic strength (raw mmCIF value) 1mM protein, 1mM oligonucleotide, 30mM NaCl, 0.2mM MgCl2；Pressure ambient NMR sample composition：1mM NCp7(12-55), 1mM DP(-)PBS, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：1mM NCp7(12-55), 1mM DP(-)PBS, 90% H2O, 10% D2O, 30mM NaCl, 0.2mM MgCl2 \| 90% H2O, 10% D2O, 30mM NaCl, 0.2mM MgCl2 NMR sample composition：2mM NCp7(12-55), 1mM DP(-)PBS, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：2mM NCp7(12-55), 1mM DP(-)PBS, 90% H2O, 10% D2O, 30mM NaCl, 0.2mM MgCl2 \| 90% H2O, 10% D2O, 30mM NaCl, 0.2mM MgCl2	Resolution not provided

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 2EXF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A9M G48H MUTANT OF HIV-1 PROTEASE IN COMPLEX WITH A PEPTIDIC INHIBITOR U-89360E Deposited 1998-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 69–167（99 aa） Chain B 69–167（99 aa）	Mutation：G48H Mutation：G48H	U0E N-[[1-[N-ACETAMIDYL]-[1-CYCLOHEXYLMETHYL-2-HYDROXY-4-ISOPROPYL]-BUT-4-YL]-CARBONYL]-GLUTAMINYL-ARGINYL-AMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.8；THE PROTEIN SOLUTION CONTAINED 6.5 MG/ML MUTANT HIV-1 PROTEASE IN 20 MM SODIUM ACETATE, 1 MM DITHIOTHREITOL, PH 5.5, WITH A 10-FOLD MOLAR EXCESS OF INHIBITOR. THE RESERVOIR SOLUTIONS FOR THE VAPOR DIFFUSION CONTAINED 10% DIMETHYLSULFOXIDE, 30 MM B-MERCAPTOETHANOL AND 4% 2-PROPANOL IN ADDITION TO THE PRECIPITANT. THE MOST FAVORABLE CRYSTALLIZATION CONDITIONS WERE 42% SATURATED AMMONIUM SULFATE, PH 6.8., vapor diffusion	Resolution 2.30 Å
1G35 CRYSTAL STRUCTURE OF HIV-1 PROTEASE IN COMPLEX WITH INHIBITOR, AHA024 Deposited 2000-10-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 69–167（99 aa） Chain B 69–167（99 aa）	Not recorded	AHF 2-[4-(HYDROXY-METHOXY-METHYL)-BENZYL]-7-(4-HYDROXYMETHYL-BENZYL)-1,1-DIOXO-3,6-BIS-PHENOXYMETHYL-1LAMBDA6-[1,2,7]THIADIAZEPANE-4,5-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；50 mM MES, 0.4 M NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.230
1GNM HIV-1 PROTEASE MUTANT WITH VAL 82 REPLACED BY ASP (V82D) COMPLEXED WITH U89360E (INHIBITOR) Deposited 1996-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 69–167（99 aa） Chain B 69–167（99 aa）	Mutation：V82D Mutation：V82D	U0E N-[[1-[N-ACETAMIDYL]-[1-CYCLOHEXYLMETHYL-2-HYDROXY-4-ISOPROPYL]-BUT-4-YL]-CARBONYL]-GLUTAMINYL-ARGINYL-AMIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1GNN HIV-1 PROTEASE MUTANT WITH VAL 82 REPLACED BY ASN (V82N) COMPLEXED WITH U89360E (INHIBITOR) Deposited 1996-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 69–167（99 aa） Chain B 69–167（99 aa）	Mutation：V82N Mutation：V82N	U0E N-[[1-[N-ACETAMIDYL]-[1-CYCLOHEXYLMETHYL-2-HYDROXY-4-ISOPROPYL]-BUT-4-YL]-CARBONYL]-GLUTAMINYL-ARGINYL-AMIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1GNO HIV-1 PROTEASE (WILD TYPE) COMPLEXED WITH U89360E (INHIBITOR) Deposited 1996-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 69–167（99 aa） Chain B 69–167（99 aa）	Not recorded	U0E N-[[1-[N-ACETAMIDYL]-[1-CYCLOHEXYLMETHYL-2-HYDROXY-4-ISOPROPYL]-BUT-4-YL]-CARBONYL]-GLUTAMINYL-ARGINYL-AMIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1HVI INFLUENCE OF STEREOCHEMISTRY ON ACTIVITY AND BINDING MODES FOR C2 SYMMETRY-BASED DIOL INHIBITORS OF HIV-1 PROTEASE Deposited 1994-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 69–167（99 aa） Chain B 69–167（99 aa）	Not recorded	A77 N-{1-BENZYL-(2R,3S)-2,3-DIHYDROXY-4-[3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRYLAMINO]-5-PHENYL-PENTYL}-3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRAMIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1KJH SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE COMPLEXES Deposited 2001-12-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 723–732（10 aa） Fragment：RNASE H-INTEGRASE SUBSTRATE PEPTIDE, RESIDUES 723-732	Not recorded	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；AMMONIUM SULPHATE, SODIUM CITRATE, SODIUM PHOSPHATE, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.227
1NPA crystal structure of HIV-1 protease-hup Deposited 2003-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 69–167（99 aa） Fragment：protease, residue 69-167 Chain B 69–167（99 aa） Fragment：protease, residue 69-167	Not recorded	3NH (3S)-TETRAHYDROFURAN-3-YL (1R,2S)-3-[4-((1R)-2-{[(S)-AMINO(HYDROXY)METHYL]OXY}-2,3-DIHYDRO-1H-INDEN-1-YL)-2-BENZYL-3-OXOPYRROLIDIN-2-YL]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；298 K；0.1 M NaAc, 0.5 M NaCl, 1mM DTT, 3mM NaN3, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å
1NPV Crystal structure of HIV-1 protease complexed with LDC271 Deposited 2003-01-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 69–167（99 aa） Fragment：HIV protease Chain B 69–167（99 aa） Fragment：HIV protease	Not recorded	L27 {1-BENZYL-3-[2-BENZYL-3-OXO-4-(1-OXO-1,2,3,4-TETRAHYDRO- ISOQUINOLIN-4-YL)-2,3-DIHYDRO-1H-PYRROL-2-YL]-2- HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；600mM NaCl, 100mM Sodium Acetate buffer at pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.260
1NPW Crystal structure of HIV protease complexed with LGZ479 Deposited 2003-01-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 69–167（99 aa） Fragment：HIV-1 PROTEASE Chain B 69–167（99 aa） Fragment：HIV-1 PROTEASE	Not recorded	LGZ CARBAMIC ACID 1-{5-BENZYL-5-[2-HYDROXY-4-PHENYL-3-(TETRAHYDRO-FURAN- 3-YLOXYCARBONYLAMINO)-BUTYL]-4-OXO-4,5-DIHYDRO-1H-PYRROL-3-YL}- INDAN-2-YL ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；600mM NaCl, 100mM Sodium Acetate buffer, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å
1T7K Crystal Structure of HIV Protease complexed with Arylsulfonamide azacyclic urea Deposited 2004-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 69–167（99 aa） Fragment：HIV Protease Chain B 69–167（99 aa） Fragment：HIV Protease	Not recorded	BH0 3-({5-BENZYL-6-HYDROXY-2,4-BIS-(4-HYDROXY-BENZYL)-3-OXO-[1,2,4]-TRIAZEPANE-1-SULFONYL)-BENZONITRILE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；293 K；0.1M sodium acetate, 0.6M NaCl, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.277
1YT9 HIV Protease with oximinoarylsulfonamide bound Deposited 2005-02-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 69–167（99 aa） Fragment：HIV protease Chain B 69–167（99 aa） Fragment：HIV protease	Not recorded	OIS (S)-N-((2S,3R)-3-HYDROXY-4-(4-((E)-(HYDROXYIMINO)METHYL)-N-ISOBUTYLPHENYLSULFONAMIDO)-1-PHENYLBUTAN-2-YL)-3-METHYL-2-(3 -((2-METHYLTHIAZOL-4-YL)METHYL)-2-OXOIMIDAZOLIDIN-1-YL)BUTANAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；nacl, acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.00 Å R-free 0.338
1ZP8 HIV Protease with inhibitor AB-2 Deposited 2005-05-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 69–167（99 aa） Fragment：HIV Protease	Not recorded	AB2 [1-((1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL)-1H-1,2,3-TRIAZOL-4-YL]METHYL (1R,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YLCARBAMATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；1.34 M Ammonium Sulfate, 0.1 M Na Acetate, pH 4.8-5.4, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.02 Å R-free 0.326
1ZPA HIV Protease with Scripps AB-3 Inhibitor Deposited 2005-05-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 69–167（99 aa） Fragment：HIV Protease	Not recorded	A83 TERT-BUTYL 4-[({[1-((1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL)-1H-1,2,3-TRIAZOL-4-YL]METHYL}AMINO)CARBONYL]BENZYLCARBAMATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；1.34 M Ammonium Sulfate, 0.1 M Na Acetate, pH 4.8-5.4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.02 Å
2FDE Wild type HIV protease bound with GW0385 Deposited 2005-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 500–598（99 aa） Fragment：protease Chain B 500–598（99 aa） Fragment：protease	Not recorded	K POTASSIUM ION × 4 385 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL [(1S,2R)-3-[(1,3-BENZODIOXOL-5-YLSULFONYL)(ISOBUTYL)AMINO]-2-HYDROXY-1-{4-[(2-METHYL-1,3-THIAZOL-4-YL)METHOXY]BENZYL}PROPYL]CARBAMATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.280
2G69 Structure of Unliganded HIV-1 Protease F53L Mutant Deposited 2006-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–99（99 aa） Fragment：HIV-1 protease monomer	Mutation：Q7K, L33I, F53L, L63I, C67A, C95A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；The reservoir contained 0.2 M sodium citrate, phosphate buffer (pH = 6.0-6.4), 10% DMSO, and 20-30% saturated ammonium sulfate as a precipitant., VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.35 Å R-free 0.234
2HNZ Crystal Structure of E138K Mutant HIV-1 Reverse Transcriptase in Complex with PETT-2 Deposited 2006-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 605–1026（422 aa） Fragment：P51	Mutation：E138K	PO4 PHOSPHATE ION × 2 PC0 1-[2-(4-ETHOXY-3-FLUOROPYRIDIN-2-YL)ETHYL]-3-(5-METHYLPYRIDIN-2-YL)THIOUREA × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.00 Å R-free 0.277
2HS1 Ultra-high resolution X-ray crystal structure of HIV-1 protease V32I mutant with TMC114 (darunavir) inhibitor Deposited 2006-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 500–598（99 aa） Fragment：HIV-1 protease (residues 500-598) Chain B 500–598（99 aa） Fragment：HIV-1 protease (residues 500-598)	Mutation：Q7K, V32I, L33I, L63I, C67A, C95A Mutation：Q7K, V32I, L33I, L63I, C67A, C95A	CL CHLORIDE ION × 3 017 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE × 2 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；1-1.5 M NaCl; Molar Protein:Inhibitor ratio = 1:20, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 0.84 Å R-free 0.149
2HS2 Crystal structure of M46L mutant of HIV-1 protease complexed with TMC114 (darunavir) Deposited 2006-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 500–598（99 aa） Fragment：HIV-1 protease (residues 500-598) Chain B 500–598（99 aa） Fragment：HIV-1 protease (residues 500-598)	Mutation：Q7K, L33I, M46L, L63I, C67A, C95A Mutation：Q7K, L33I, M46L, L63I, C67A, C95A	CL CHLORIDE ION × 2 017 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE × 2 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.8；295 K；25% NaCl; Molar protein:inhibitor ratio 1:2., pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.22 Å R-free 0.195
2I4D Crystal structure of WT HIV-1 protease with GS-8373 Deposited 2006-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 500–598（99 aa） Chain B 500–598（99 aa）	Not recorded	QFI ({4-[(2S,3R)-2-({[(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YLOXY]CARBONYL}AMINO)-3-HYDROXY-4-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}BUTYL]PHENOXY}METHYL)PHOSPHONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2M Mg Acetate, 0.1M Na cacodylate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.50 Å R-free 0.274
2I4U HIV-1 protease with TMC-126 Deposited 2006-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 500–598（99 aa） Chain B 500–598（99 aa）	Not recorded	DJR (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL [(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]CARBAMATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；0.4 M Sodium Potassium Tartrate, pH 7.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.50 Å R-free 0.250
2I4V HIV-1 protease I84V, L90M with TMC126 Deposited 2006-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 500–598（99 aa） Chain B 500–598（99 aa）	Mutation：I84V, L90M Mutation：I84V, L90M	DJR (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL [(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]CARBAMATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；0.4 M Sodium Potassium Tartrate, pH 7.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.50 Å R-free 0.256
2I4W HIV-1 protease WT with GS-8374 Deposited 2006-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 500–598（99 aa） Chain B 500–598（99 aa）	Not recorded	KGQ DIETHYL ({4-[(2S,3R)-2-({[(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YLOXY]CARBONYL}AMINO)-3-HYDROXY-4-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}BUTYL]PHENOXY}METHYL)PHOSPHONATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；0.2M Mg Acetate, 0.1M Na Cacodylate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.55 Å R-free 0.252
2I4X HIV-1 Protease I84V, L90M with GS-8374 Deposited 2006-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 500–598（99 aa） Chain B 500–598（99 aa）	Mutation：I84V, L90M Mutation：I84V, L90M	KGQ DIETHYL ({4-[(2S,3R)-2-({[(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YLOXY]CARBONYL}AMINO)-3-HYDROXY-4-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}BUTYL]PHENOXY}METHYL)PHOSPHONATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；0.4 M Sodium Potassium Tartrate, pH 7.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.55 Å R-free 0.272
2IDW Crystal structure analysis of HIV-1 protease mutant V82A with a potent non-peptide inhibitor (UIC-94017) Deposited 2006-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 500–598（99 aa） Fragment：residues 500-598 Chain B 500–598（99 aa） Fragment：residues 500-598	Mutation：Q7K, L33I, L63I, C67A, V82A, C95A, Q107K, L133I, L163I, C167A, V182A, C195A Mutation：Q7K, L33I, L63I, C67A, V82A, C95A, Q107K, L133I, L163I, C167A, V182A, C195A	CL CHLORIDE ION × 1 PO4 PHOSPHATE ION × 4 DMS DIMETHYL SULFOXIDE × 1 ACY ACETIC ACID × 6 GOL GLYCEROL × 1 017 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；AMMONIUM SULFATE, CITRIC PHOSPHATE, DMSO, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.10 Å R-free 0.145
2IEN Crystal structure analysis of HIV-1 protease with a potent non-peptide inhibitor (UIC-94017) Deposited 2006-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 500–598（99 aa） Fragment：residues 500-598 Chain B 500–598（99 aa） Fragment：residues 500-598	Mutation：Q7K, L33I, L63I, C67A, C95A, Q107K, L133I, L163I, C167A, C195A Mutation：Q7K, L33I, L63I, C67A, C95A, Q107K, L133I, L163I, C167A, C195A	NA SODIUM ION × 1 CL CHLORIDE ION × 2 ACY ACETIC ACID × 2 017 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；sodium chloride, sodium acetate, DMSO, dioxane, pH 4.80, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.30 Å R-free 0.205
2IEO Crystal structure analysis of HIV-1 protease mutant I84V with a potent non-peptide inhibitor (UIC-94017) Deposited 2006-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 500–598（99 aa） Fragment：residues 500-598 Chain B 500–598（99 aa） Fragment：residues 500-598	Mutation：Q7K, L33I, L63I, C67A, I84V, C95A, Q107K, L133I, L163I, C167A, C195A Mutation：Q7K, L33I, L63I, C67A, I84V, C95A, Q107K, L133I, L163I, C167A, C195A	CL CHLORIDE ION × 3 NA SODIUM ION × 1 017 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；SODIUM CHLORIDE, CITRATE PHOSPHATE, DMSO, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.53 Å R-free 0.196

27 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POL_HV1PV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 2–44； UniProt 389–431

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2exf
Deposition date deposition_date	2005-11-08
Structure title title	Solution structure of the HIV-1 nucleocapsid (NCp7(12-55)) complexed with the DNA (-) Primer Binding Site
Keywords keywords	protein-DNA complex, stem-loop, bulge, zinc-finger, Viral Protein-DNA COMPLEX; Viral Protein/DNA
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	13.24 Å
Radius of gyration Rg (electron density) rg_electron	13.13 Å
Forward intensity I(0) i0	249938000.00
Molecular weight molecular_weight	94064.0 kDa
Excluded volume excluded_volume	101820 Å³
Envelope volume envelope_volume	20377 Å³
Hydration-shell volume shell_volume	12122 Å³
Envelope diameter envelope_diameter	51.5 Å
Shell Rg shell_rg	20.10 Å
Envelope Rg envelope_rg	14.93 Å
Shape Rg shape_rg	13.07 Å
Total Rg total_rg	13.44 Å
Total atoms total_atoms	11220
Residues n_residues	580
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

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

Maximum dimension Dmax dmax	46.3 Å
Rg (real space) rg_real	13.28 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	2.4990e+08
I(0) uncertainty (real space) i0_real_error	2.7800e+06
Rg (reciprocal space) rg_reciprocal	13.27 Å
I(0) (reciprocal space) i0_reciprocal	249900000.0000
Solution quality estimate total_estimate	0.6908
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.2 Å
Skewness Skewness skewness	0.398
Kurtosis Kurtosis kurtosis	-0.291
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	211500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.782; Stabil: 1.000; Sysdev: 0.256; Positv: 1.000; Valcen: 0.867; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	5'-D(GPTPCPCPCPTPGPTPTPCPGPGPGPC)-3'
Molecular weight formula_weight	4263.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	11220

GTCCCTGTTCGGGC

Entity 2 Entity 2 polymer

Description description	Nucleocapsid protein* (NC*)
Molecular weight formula_weight	5022.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQAN

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2exfa1
Class class	g — Small proteins
Fold Fold fold	g.40 — Retrovirus zinc finger-like domains
Superfamily Superfamily superfamily	g.40.1 — Retrovirus zinc finger-like domains
Family Family family	g.40.1.1 — Retrovirus zinc finger-like domains

Domain ID domain_id	d2exfa2
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

CATH v4.4 (1 domains)

Domain ID domain_id	2exfA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	60 — HIV-1 Nucleocapsid Protein
Homologous superfamily homologous superfamily	10 — Zinc finger, CCHC-type

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

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

fit	/app/data/saxs_computation/ex/2exf/2exf.fit
pddf	/app/data/pr_computation/ex/2exf/2exf.pr.out
profile	/app/data/saxs_computation/ex/2exf/2exf.dat

Solution structure of the HIV-1 nucleocapsid (NCp7(12-55)) complexed with the DNA (-) Primer Binding Site

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

Nucleocapsid protein* (NC*)

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)