SAXSdb — 3lp3

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

p15

Human immunodeficiency virus type 1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1014–1149	Fragment：residues 1014-1149	MN MANGANESE (II) ION × 2 LP9 3-[4-(diethylamino)phenoxy]-6-(ethoxycarbonyl)-5,8-dihydroxy-7-oxo-7,8-dihydro-1,8-naphthyridin-1-ium × 1	X-RAY DIFFRACTION X-ray crystallization conditions：hanging drop；pH 6.8；298 K；0.1 M Sodium citrate pH 5.0, 15-20% PEG 8000, hanging drop, temperature 298K	Resolution 2.80 Å R-free 0.288
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1014–1149	Fragment：residues 1014-1149	MN MANGANESE (II) ION × 2 LP9 3-[4-(diethylamino)phenoxy]-6-(ethoxycarbonyl)-5,8-dihydroxy-7-oxo-7,8-dihydro-1,8-naphthyridin-1-ium × 1	X-RAY DIFFRACTION X-ray crystallization conditions：hanging drop；pH 6.8；298 K；0.1 M Sodium citrate pH 5.0, 15-20% PEG 8000, hanging drop, temperature 298K	Resolution 2.80 Å R-free 0.288
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1014–1149 Chain B； UniProt 1014–1149	Fragment：residues 1014-1149	MN MANGANESE (II) ION × 4 LP9 3-[4-(diethylamino)phenoxy]-6-(ethoxycarbonyl)-5,8-dihydroxy-7-oxo-7,8-dihydro-1,8-naphthyridin-1-ium × 2	X-RAY DIFFRACTION X-ray crystallization conditions：hanging drop；pH 6.8；298 K；0.1 M Sodium citrate pH 5.0, 15-20% PEG 8000, hanging drop, temperature 298K	Resolution 2.80 Å R-free 0.288

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 3LP3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3TH9 Crystal Structure of HIV-1 Protease Mutant Q7K V32I L63I with a cyclic sulfonamide inhibitor Deposited 2011-08-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 489–587（99 aa） Fragment：HIV protease Chain B 489–587（99 aa） Fragment：HIV protease	Mutation：Q7K V32I L63I Mutation：Q7K V32I L63I	9Y9 tert-butyl {(2S,3R)-4-[(4S)-7-fluoro-4-methyl-1,1-dioxido-4,5-dihydro-1,2-benzothiazepin-2(3H)-yl]-3-hydroxy-1-phenylbutan-2-yl}carbamate × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；295 K；0.1 M sodium acetate buffer, 0.4M NaCl, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.34 Å R-free 0.190
3VFA Crystal Structure of HIV-1 Protease Mutant V82A with novel P1'-Ligands GRL-02031 Deposited 2012-01-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 489–587（99 aa） Fragment：UNP residues 501-599 Chain B 489–587（99 aa） Fragment：UNP residues 501-599	Mutation：Q507K, L33I5, L563I, C567A, V582A, C595A Mutation：Q507K, L33I5, L563I, C567A, V582A, C595A	031 (3aS,5R,6aR)-hexahydro-2H-cyclopenta[b]furan-5-yl [(1S,2R)-1-benzyl-2-hydroxy-3-([(4-methoxyphenyl)sulfonyl]{[(2R)-5-oxopyrrolidin-2-yl]methyl}amino)propyl]carbamate × 1 NA SODIUM ION × 1 CL CHLORIDE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；0.6M NaCl, 0.1M Sodium Acetate buffer pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.43 Å R-free 0.218
4I8W Crystal structure of wild type HIV-1 protease in complex with non-peptidic inhibitor, GRL007 Deposited 2012-12-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 489–587（99 aa） Chain B 489–587（99 aa）	Not recorded	G07 4-{[(2R,3S)-3-({[(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yloxy]carbonyl}amino)-2-hydroxy-4-phenylbutyl](2-methylpropyl)sulfamoyl}benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；1.6 M ammonium sulfate (precipitant) in 0.1 M BICINE buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.96 Å R-free 0.233
4I8Z Crystal structure of wild type HIV-1 protease in complex with non-peptidic inhibitor, GRL008 Deposited 2012-12-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 489–587（99 aa） Chain B 489–587（99 aa）	Not recorded	G08 (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-4-{[(4-carbamoylphenyl)sulfonyl](2-methylpropyl)amino}-3-hydroxy-1-phenylbutan-2-yl]carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；1.6 M ammonium sulfate (precipitant) in 0.1 M BICINE buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.220
4MC1 HIV protease in complex with SA526P Deposited 2013-08-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 489–587（99 aa） Fragment：UNP residues 489-587 Chain B 489–587（99 aa） Fragment：UNP residues 489-587	Mutation：Q7K V32I L63I Mutation：Q7K V32I L63I	CL CHLORIDE ION × 3 526 (3S)-tetrahydrofuran-3-yl {(2S,3R)-4-[(4S)-4-tert-butyl-7-fluoro-1,1-dioxido-4,5-dihydro-1,2-benzothiazepin-2(3H)-yl]-3-hydroxy-1-phenylbutan-2-yl}carbamate × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.7 M sodium chloride, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.39 Å R-free 0.188
4MC2 HIV protease in complex with SA525P Deposited 2013-08-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 489–587（99 aa） Fragment：UNP residues 489-587 Chain B 489–587（99 aa） Fragment：UNP residues 489-587	Mutation：Q7K V32I L63I Mutation：Q7K V32I L63I	525 (3S)-tetrahydrofuran-3-yl {(2S,3R)-4-[(4R)-4-tert-butyl-7-fluoro-1,1-dioxido-4,5-dihydro-1,2-benzothiazepin-2(3H)-yl]-3-hydroxy-1-phenylbutan-2-yl}carbamate × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.7 M sodium chloride, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.56 Å R-free 0.207
4MC6 HIV protease in complex with SA499 Deposited 2013-08-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 489–587（99 aa） Fragment：UNP residues 489-587 Chain B 489–587（99 aa） Fragment：UNP residues 489-587	Mutation：Q7K V32I L63I Mutation：Q7K V32I L63I	23K 1-tert-butyl-3-{(2S,3R)-4-[(4R)-7-fluoro-1,1-dioxido-4-(propan-2-yl)-4,5-dihydro-1,2-benzothiazepin-2(3H)-yl]-3-hydroxy-1-phenylbutan-2-yl}urea × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.7 M sodium chloride, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.31 Å R-free 0.198
4MC9 HIV protease in complex with AA74 Deposited 2013-08-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 489–587（99 aa） Fragment：UNP residues 489-587 Chain B 489–587（99 aa） Fragment：UNP residues 489-587	Mutation：Q7K V32I L63I Mutation：Q7K V32I L63I	23L (3S)-tetrahydrofuran-3-yl {(2S,3R)-4-[(4R)-7-fluoro-1,1-dioxido-4-(propan-2-yl)-4,5-dihydro-1,2-benzothiazepin-2(3H)-yl]-3-hydroxy-1-phenylbutan-2-yl}carbamate × 2 EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.7 M sodium chloride, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.19 Å R-free 0.195
4NYF HIV integrase in complex with inhibitor Deposited 2013-12-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1199–1357（159 aa） Fragment：Integrase catalytic domain residues 1199-1357 Chain B 1199–1357（159 aa） Fragment：Integrase catalytic domain residues 1199-1357	Mutation：C56S, W131D, F139D, F185K Mutation：C56S, W131D, F139D, F185K	4BI (2S)-tert-butoxy[4-(4-chlorophenyl)-2-methylquinolin-3-yl]ethanoic acid × 1 CD CADMIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；297 K；1.2 -1.5 M Ammonium Sulfate, 100mM Na citrate pH 5.6, 50mM Cadmium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 1.90 Å R-free 0.223
4QGI X-ray crystal structure of HIV-1 protease variant G48T/L89M in complex with Saquinavir Deposited 2014-05-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 489–587（99 aa） Fragment：HIV-1 Protease Chain A, unp residues 489-587 Chain B 489–587（99 aa） Fragment：HIV-1 Protease Chain A, unp residues 489-587	Mutation：G48T, L89M Mutation：G48T, L89M	ROC (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1 M Sodium citrate, 20% 2-propanol, 20% PEG 4000 , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.246
5K14 HIV-1 Reverse Transcriptase in complex with a 2,6-difluorophenyl DAPY analog Deposited 2016-05-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 588–1027（440 aa）	Not recorded	IB1 4-{[4-(2,6-difluoro-4-methoxybenzene-1-carbonyl)pyrimidin-2-yl]amino}benzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.0M K/Na tartrate 100mM MES pH 6.0	Resolution 2.40 Å R-free 0.261
6Y9V Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-8,13) Deposited 2020-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 133–352（220 aa） Chain B 133–352（220 aa） Chain C 133–352（220 aa） Chain D 133–352（220 aa） Chain G 133–352（220 aa） Chain H 133–352（220 aa） Chain N 133–352（220 aa） Chain Y 133–352（220 aa） Chain d 133–352（220 aa） Chain e 133–352（220 aa） Chain j 133–352（220 aa） Chain k 133–352（220 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.90 Å
6Y9W Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,8) Deposited 2020-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 133–352（220 aa） Chain B 133–352（220 aa） Chain C 133–352（220 aa） Chain D 133–352（220 aa） Chain G 133–352（220 aa） Chain H 133–352（220 aa） Chain N 133–352（220 aa） Chain Y 133–352（220 aa） Chain d 133–352（220 aa） Chain e 133–352（220 aa） Chain j 133–352（220 aa） Chain k 133–352（220 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6Y9X Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,7) Deposited 2020-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 133–352（220 aa） Chain B 133–352（220 aa） Chain C 133–352（220 aa） Chain D 133–352（220 aa） Chain G 133–352（220 aa） Chain H 133–352（220 aa） Chain N 133–352（220 aa） Chain Y 133–352（220 aa） Chain d 133–352（220 aa） Chain e 133–352（220 aa） Chain j 133–352（220 aa） Chain k 133–352（220 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
6Y9Y Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-7,13) Deposited 2020-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 133–352（220 aa） Chain B 133–352（220 aa） Chain C 133–352（220 aa） Chain D 133–352（220 aa） Chain G 133–352（220 aa） Chain H 133–352（220 aa） Chain N 133–352（220 aa） Chain Y 133–352（220 aa） Chain d 133–352（220 aa） Chain e 133–352（220 aa） Chain j 133–352（220 aa） Chain k 133–352（220 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.10 Å
6Y9Z Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,9) Deposited 2020-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 133–352（220 aa） Chain B 133–352（220 aa） Chain C 133–352（220 aa） Chain D 133–352（220 aa） Chain G 133–352（220 aa） Chain H 133–352（220 aa） Chain N 133–352（220 aa） Chain Y 133–352（220 aa） Chain d 133–352（220 aa） Chain e 133–352（220 aa） Chain j 133–352（220 aa） Chain k 133–352（220 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
9JA0 The capsid protein of HIV 1 Deposited 2024-08-23	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 × 12 PDB declaration: dodecameric	Chain A 133–353（221 aa） Chain B 133–353（221 aa） Chain C 133–353（221 aa） Chain D 133–353（221 aa） Chain E 133–353（221 aa） Chain F 133–353（221 aa） Chain G 133–353（221 aa） Chain H 133–353（221 aa） Chain I 133–353（221 aa） Chain J 133–353（221 aa） Chain K 133–353（221 aa） Chain L 133–353（221 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å

17 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POL_HV1LW
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–138； UniProt 1014–1149 Author chain B； PDBConstruct 3–138； UniProt 1014–1149

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	3lp3
Deposition date deposition_date	2010-02-04
Structure title title	p15 HIV RNaseH domain with inhibitor MK3
Keywords keywords	;Reverse Transcriptase, RNase H, HIV, AIDS, Capsid maturation, DNA integration, DNA-directed DNA polymerase, Endonuclease, Host cytoplasm, Host nucleus, Multifunctional enzyme, RNA-binding, RNA-directed DNA polymerase, Viral nucleoprotein, Virion, VIRAL PROTEIN ;; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	20.53 Å
Radius of gyration Rg (electron density) rg_electron	19.65 Å
Forward intensity I(0) i0	15085700.00
Molecular weight molecular_weight	29669.0 kDa
Excluded volume excluded_volume	37371 Å³
Envelope volume envelope_volume	44845 Å³
Hydration-shell volume shell_volume	18999 Å³
Envelope diameter envelope_diameter	67.7 Å
Shell Rg shell_rg	25.87 Å
Envelope Rg envelope_rg	19.97 Å
Shape Rg shape_rg	19.65 Å
Total Rg total_rg	20.59 Å
Total atoms total_atoms	2084
Residues n_residues	262
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	65.2 Å
Rg (real space) rg_real	20.46 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	1.5090e+07
I(0) uncertainty (real space) i0_real_error	1.7020e+05
Rg (reciprocal space) rg_reciprocal	20.48 Å
I(0) (reciprocal space) i0_reciprocal	15090000.0000
Solution quality estimate total_estimate	0.9076
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.6 Å
Skewness Skewness skewness	0.200
Kurtosis Kurtosis kurtosis	-0.534
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2262000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	p15
Molecular weight formula_weight	15175.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2104

GSYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKILFL

来源 Source

来源生物 organism	Human immunodeficiency virus type 1
通用名 common_name	HIV-1
NCBI Class编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	3-[4-(diethylamino)phenoxy]-6-(ethoxycarbonyl)-5,8-dihydroxy-7-oxo-7,8-dihydro-1,8-naphthyridin-1-ium
Molecular weight formula_weight	413.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3lp3a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.1 — Ribonuclease H

Domain ID domain_id	d3lp3b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.1 — Ribonuclease H

CATH v4.4 (2 domains)

Domain ID domain_id	3lp3A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	3lp3B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

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8. Citations (1)

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Unit-cell length a length_a	51.256 Å
Unit-cell length b length_b	51.256 Å
Unit-cell length c length_c	112.773 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	34.880 Å
R factor r_factor	0.2323
R_work r_work	0.2295
R_free r_free	0.2883

fit	/app/data/saxs_computation/lp/3lp3/3lp3.fit
pddf	/app/data/pr_computation/lp/3lp3/3lp3.pr.out
profile	/app/data/saxs_computation/lp/3lp3/3lp3.dat

p15 HIV RNaseH domain with inhibitor MK3

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

p15

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