SAXSdb — 4ej8

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

Protease

Human immunodeficiency virus 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 490–588 Chain B； UniProt 490–588	Fragment：UNP residues 490-588 Mutation：Q7K, L33I, L63I, C67A, C95A	DMS DIMETHYL SULFOXIDE × 5 EDO 1,2-ETHANEDIOL × 4 1F1 1H-indole-6-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；298 K；0.1 M Tris, pH 7.5, 28% PEG4000, 10% DMSO, VAPOR DIFFUSION, temperature 298K	Resolution 2.35 Å R-free 0.243

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 4EJ8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1E28 Nonstandard peptide binding of HLA-B*5101 complexed with HIV immunodominant epitope KM2(TAFTIPSI) Deposited 2000-05-18	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 282–289（8 aa） Fragment：EXTRACELLULAR RESIDUES 282-289	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 3.00 Å R-free 0.253
1HXW HIV-1 PROTEASE DIMER COMPLEXED WITH A-84538 Deposited 1997-01-24	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 24–122（99 aa） Chain B 24–122（99 aa）	Not recorded	RIT RITONAVIR × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1P7Q Crystal Structure of HLA-A2 Bound to LIR-1, a Host and Viral MHC Receptor Deposited 2003-05-05	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 463–471（9 aa） Fragment：residue 463-471	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 4000, Sodium Acetate, Tris, L-Cysteine, Triton X-100, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.40 Å R-free 0.309
1PRO HIV-1 PROTEASE DIMER COMPLEXED WITH A-98881 Deposited 1995-07-18	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 24–122（99 aa） Chain B 24–122（99 aa）	Not recorded	A88 (5R,6R)-2,4-BIS-(4-HYDROXY-3-METHOXYBENZYL)-1,5-DIBENZYL-3-OXO-6-HYDROXY-1,2,4-TRIAZACYCLOHEPTANE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å R-free 0.310
1Q94 Structures of HLA-A*1101 in complex with immunodominant nonamer and decamer HIV-1 epitopes clearly reveal the presence of a middle anchor residue Deposited 2003-08-22	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 745–753（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；PEG 4000,sodium acetate,sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 2.40 Å R-free 0.272
1Q94 Structures of HLA-A*1101 in complex with immunodominant nonamer and decamer HIV-1 epitopes clearly reveal the presence of a middle anchor residue Deposited 2003-08-22	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 F 745–753（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；PEG 4000,sodium acetate,sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 2.40 Å R-free 0.272
1VIJ HIV-1 PROTEASE COMPLEXED WITH THE INHIBITOR HOE/BAY 793 HEXAGONAL FORM Deposited 1997-05-07	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 56–154（99 aa） Chain B 56–154（99 aa）	Not recorded	BAY N-(1-BENZYL-2,3-DIHYDROXY-4-{3-METHYL-2-[2-(2-METHYL-PROPANE-2-SULFONYLMETHYL)-3-NAPHTHALEN-1-YL-PROPIONYLAMINO]-BUTYRYLAMINO}-5-PHENYL-PENTYL)-3-METHYL-2-[2-(2-METHYL-PROPANE-2-SULFONYLMETHYL)-3-NAPHTHALEN-1-YL-PROPIONYLAMINO]-BUTYRAMIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1VIK HIV-1 PROTEASE COMPLEXED WITH THE INHIBITOR HOE/BAY 793 ORTHORHOMBIC FORM Deposited 1997-05-07	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 56–154（99 aa） Chain B 56–154（99 aa）	Not recorded	BAY N-(1-BENZYL-2,3-DIHYDROXY-4-{3-METHYL-2-[2-(2-METHYL-PROPANE-2-SULFONYLMETHYL)-3-NAPHTHALEN-1-YL-PROPIONYLAMINO]-BUTYRYLAMINO}-5-PHENYL-PENTYL)-3-METHYL-2-[2-(2-METHYL-PROPANE-2-SULFONYLMETHYL)-3-NAPHTHALEN-1-YL-PROPIONYLAMINO]-BUTYRAMIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
3W39 Crystal structure of HLA-B*5201 in complexed with HIV immunodominant epitope (TAFTIPSI) Deposited 2012-12-13	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 716–723（8 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M sodium acetate, 0.1M Bis Tris propane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.10 Å R-free 0.347
3W39 Crystal structure of HLA-B*5201 in complexed with HIV immunodominant epitope (TAFTIPSI) Deposited 2012-12-13	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 F 716–723（8 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M sodium acetate, 0.1M Bis Tris propane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.10 Å R-free 0.347
4EJD HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment 1F1 in the outside/top of flap Deposited 2012-04-06	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 A 490–588（99 aa） Fragment：UNP residues 490-588 Chain B 490–588（99 aa） Fragment：UNP residues 490-588	Not recorded	BME BETA-MERCAPTOETHANOL × 3 1F1 1H-indole-6-carboxylic acid × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；0.2 M potassium bromide, 0.2 M potassium thiocyanate, 3% PGA-LM, 3% MPD, 10% DMSO, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.10 Å R-free 0.176
4EJK HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment 1F1-N in the outside/top of flap Deposited 2012-04-06	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 A 490–588（99 aa） Fragment：UNP residues 490-588 Chain B 490–588（99 aa） Fragment：UNP residues 490-588	Not recorded	IOP INDOLYLPROPIONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；298 K；1.0 M sodium formate, 10% DMSO, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, temperature 298K	Resolution 1.79 Å R-free 0.252
4EJL Apo HIV Protease (PR) dimer in closed form with fragment 1F1-N in the outside/top of flap Deposited 2012-04-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 490–588（99 aa） Fragment：UNP residues 490-588 Chain B 490–588（99 aa） Fragment：UNP residues 490-588	Mutation：Q7K, L33I, L63I, C67A, C95A Mutation：Q7K, L33I, L63I, C67A, C95A	PEG DI(HYDROXYETHYL)ETHER × 1 DMS DIMETHYL SULFOXIDE × 2 GOL GLYCEROL × 4 IOP INDOLYLPROPIONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；298 K；0.8 M sodium formate, 15% PEG4000, 0.1 M sodium acetate, pH 5.5, VAPOR DIFFUSION, temperature 298K	Resolution 2.44 Å R-free 0.245
4K4P TL-3 inhibited Trp6Ala HIV Protease Deposited 2013-04-12	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 1–99（99 aa） Chain B 1–99（99 aa）	Mutation：W6A Mutation：W6A	NO3 NITRATE ION × 1 3TL benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5；298 K；0.1M NaOAc pH 5.0, 2.5M NaNO3, vapor diffusion, temperature 298K	Resolution 2.31 Å R-free 0.234
4K4Q TL-3 inhibited Trp6Ala HIV Protease with 3-bromo-2,6-dimethoxybenzoic acid bound in flap site Deposited 2013-04-12	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 1–99（99 aa） Chain B 1–99（99 aa）	Mutation：W6A Mutation：W6A	NO3 NITRATE ION × 6 BME BETA-MERCAPTOETHANOL × 1 DMS DIMETHYL SULFOXIDE × 2 3TL benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate × 1 06B 3-bromo-2,6-dimethoxybenzoic acid × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5；298 K；0.1M NaOAc pH 5.0, 2.5M NaNO3, vapor diffusion, temperature 298K	Resolution 1.80 Å R-free 0.230
4K4R TL-3 inhibited Trp6Ala HIV Protease with 1-bromo-2-napthoic acid bound in exosite Deposited 2013-04-12	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 1–99（99 aa） Chain B 1–99（99 aa）	Mutation：W6A Mutation：W6A	DMS DIMETHYL SULFOXIDE × 1 27B 1-bromonaphthalene-2-carboxylic acid × 2 NO3 NITRATE ION × 5 3TL benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate × 1 BR BROMIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5；298 K；0.1M NaOAc pH 5.0, 2.5M NaNO3, vapor diffusion, temperature 298K	Resolution 1.80 Å R-free 0.235
9K2R Human T cell receptor (TRAV2401/TRBV2701) in complex with HLA-C*1202 and IY11 peptide Deposited 2024-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 897–907（11 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH7.0, 1.6M ammonium sulfate, 0.2M sodium thiocyanate	Resolution 2.98 Å R-free 0.233
9K2R Human T cell receptor (TRAV2401/TRBV2701) in complex with HLA-C*1202 and IY11 peptide Deposited 2024-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 897–907（11 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH7.0, 1.6M ammonium sulfate, 0.2M sodium thiocyanate	Resolution 2.98 Å R-free 0.233
9K2R Human T cell receptor (TRAV2401/TRBV2701) in complex with HLA-C*1202 and IY11 peptide Deposited 2024-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 897–907（11 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH7.0, 1.6M ammonium sulfate, 0.2M sodium thiocyanate	Resolution 2.98 Å R-free 0.233
9K2S Killer cell immunoglobulin-like receptor 2DL2 in complex with HLA-C*1202 and IY10 peptide Deposited 2024-10-18	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 D 897–906（10 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M K/Na tartrate, 20% PEG 3350	Resolution 2.40 Å R-free 0.299
9K2T Crystal structure of HLA-C*1202 in complex with IY10 peptide Deposited 2024-10-18	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 897–906（10 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；PEG	Resolution 2.20 Å R-free 0.243

17 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POL_HV1Z2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 490–588 Author chain B； PDBConstruct 1–99； UniProt 490–588

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	4ej8
Deposition date deposition_date	2012-04-06
Structure title title	Apo HIV Protease (PR) dimer in closed form with fragment 1F1 in the outside/top of flap
Keywords keywords	apo protease, allostery, fragment binding, closed form, HYDROLASE; HYDROLASE
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	18.80 Å
Radius of gyration Rg (electron density) rg_electron	17.83 Å
Forward intensity I(0) i0	8082490.00
Molecular weight molecular_weight	22318.0 kDa
Excluded volume excluded_volume	28703 Å³
Envelope volume envelope_volume	33226 Å³
Hydration-shell volume shell_volume	16124 Å³
Envelope diameter envelope_diameter	67.0 Å
Shell Rg shell_rg	23.45 Å
Envelope Rg envelope_rg	18.05 Å
Shape Rg shape_rg	17.82 Å
Total Rg total_rg	18.87 Å
Total atoms total_atoms	1564
Residues n_residues	198
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	67.2 Å
Rg (real space) rg_real	18.80 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	8.0820e+06
I(0) uncertainty (real space) i0_real_error	1.0280e+05
Rg (reciprocal space) rg_reciprocal	18.80 Å
I(0) (reciprocal space) i0_reciprocal	8082000.0000
Solution quality estimate total_estimate	0.8431
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.2 Å
Skewness Skewness skewness	0.370
Kurtosis Kurtosis kurtosis	-0.228
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2998000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.678; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.980

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Protease
Molecular weight formula_weight	10767.7 kDa
EC 编号 ec_number	3.4.23.16
Mutation mutation	Q7K, L33I, L63I, C67A, C95A
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	1698

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMNLPGRWKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

来源 Source

来源生物 organism	Human immunodeficiency virus 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	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	1H-indole-6-carboxylic acid
Molecular weight formula_weight	161.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	120

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4ej8a_
Class class	b — All beta proteins
Fold Fold fold	b.50 — Acid proteases
Superfamily Superfamily superfamily	b.50.1 — Acid proteases
Family Family family	b.50.1.1 — Retroviral protease (retropepsin)

Domain ID domain_id	d4ej8b_
Class class	b — All beta proteins
Fold Fold fold	b.50 — Acid proteases
Superfamily Superfamily superfamily	b.50.1 — Acid proteases
Family Family family	b.50.1.1 — Retroviral protease (retropepsin)

CATH v4.4 (2 domains)

Domain ID domain_id	4ej8A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acid Proteases

Domain ID domain_id	4ej8B00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acid Proteases

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8. Citations (1)

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Unit-cell length a length_a	28.947 Å
Unit-cell length b length_b	66.533 Å
Unit-cell length c length_c	91.713 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.347 Å
Low-resolution limit resolution_low	53.850 Å
R factor r_factor	0.1923
R_work r_work	0.1899
R_free r_free	0.2427

fit	/app/data/saxs_computation/ej/4ej8/4ej8.fit
pddf	/app/data/pr_computation/ej/4ej8/4ej8.pr.out
profile	/app/data/saxs_computation/ej/4ej8/4ej8.dat

Apo HIV Protease (PR) dimer in closed form with fragment 1F1 in the outside/top of flap

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

Protease

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