SAXSdb — 6tvu

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

Env polyprotein (Fragment)

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 heterocomplex Heteromer Protein × 6 PDB declaration: nonameric（9） Count mismatch; review required	Chain AaA； UniProt 9–46	Non-standard monomer：Yes (specific site not provided by mmCIF)	Transmembrane protein gp41 × 3 （P04582）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.6；293.15 K；PEG 4000, 2-Propanol, Citrate	Resolution 1.25 Å R-free 0.210

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 6TVU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6TVQ Structure of native gp41 derived peptide fusion inhibitor Deposited 2020-01-10	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain AaA 9–46（38 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；292.15 K；Ammonium sulfate, PEG 3350, Bis-Tris	Resolution 1.45 Å R-free 0.243

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	C7F3P9_9HIV1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AaA； PDBConstruct 2–39； UniProt 9–46

Transmembrane protein gp41

OrganismNot specified

UniProt P04582

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 heterocomplex Heteromer Protein × 6 PDB declaration: nonameric（9） Count mismatch; review required	Chain BBB； UniProt 616–645	Non-standard monomer：Yes (specific site not provided by mmCIF)	Env polyprotein (Fragment) × 3 （C7F3P9）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.6；293.15 K；PEG 4000, 2-Propanol, Citrate	Resolution 1.25 Å R-free 0.210

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 6TVU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DDH MHC CLASS I H-2DD HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND AN IMMUNODOMINANT PEPTIDE P18-I10 FROM THE HUMAN IMMUNODEFICIENCY VIRUS ENVELOPE GLYCOPROTEIN 120 Deposited 1998-06-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 311–320（10 aa） Fragment：RESIDUES 308-322	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 3.10 Å R-free 0.337
1HHG THE ANTIGENIC IDENTITY OF PEPTIDE(SLASH)MHC COMPLEXES: A COMPARISON OF THE CONFORMATION OF FIVE PEPTIDES PRESENTED BY HLA-A2 Deposited 1993-06-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 192–200（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1HHG THE ANTIGENIC IDENTITY OF PEPTIDE(SLASH)MHC COMPLEXES: A COMPARISON OF THE CONFORMATION OF FIVE PEPTIDES PRESENTED BY HLA-A2 Deposited 1993-06-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 192–200（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1QO3 Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd Deposited 1999-11-01	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 P 311–320（10 aa） Fragment：RESIDUES 318-327	Mutation：YES	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.30 Å R-free 0.238
1QO3 Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd Deposited 1999-11-01	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 P 311–320（10 aa） Fragment：RESIDUES 318-327	Mutation：YES	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.30 Å R-free 0.238
1SZT ATOMIC STRUCTURE OF A THERMOSTABLE SUBDOMAIN OF HIV-1 GP41 Deposited 1997-07-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 541–574（34 aa） Fragment：RESIDUES 546 - 579 AND 628 - 655 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG-GLY-GLY)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.269
6TVW Structure of native gp41 derived peptide fusion inhibitor Deposited 2020-01-10	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: nonameric	Chain DbD 631–644（14 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；PEG 3350, ammonium sulfate	Resolution 1.45 Å R-free 0.298
9D72 CryoEM structure of anti-MHC-I Fab M1/42 complex with H2-Dd Deposited 2024-08-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain P 311–320（10 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.67 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ENV_HV1B8
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain BBB； PDBConstruct 1–30； UniProt 616–645

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	6tvu
Deposition date deposition_date	2020-01-10
Structure title title	Structure of native gp41 derived peptide fusion inhibitor
Keywords keywords	Inhibitor, helix bundle, HIV, 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	16.95 Å
Radius of gyration Rg (electron density) rg_electron	16.49 Å
Forward intensity I(0) i0	1476740.00
Molecular weight molecular_weight	8171.0 kDa
Excluded volume excluded_volume	10212 Å³
Envelope volume envelope_volume	13431 Å³
Hydration-shell volume shell_volume	8144 Å³
Envelope diameter envelope_diameter	61.5 Å
Shell Rg shell_rg	19.68 Å
Envelope Rg envelope_rg	16.97 Å
Shape Rg shape_rg	16.44 Å
Total Rg total_rg	17.37 Å
Total atoms total_atoms	1146
Residues n_residues	66
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	63.3 Å
Rg (real space) rg_real	17.22 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	1.4770e+06
I(0) uncertainty (real space) i0_real_error	2.1290e+04
Rg (reciprocal space) rg_reciprocal	17.19 Å
I(0) (reciprocal space) i0_reciprocal	1477000.0000
Solution quality estimate total_estimate	0.7875
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.8 Å
Skewness Skewness skewness	0.635
Kurtosis Kurtosis kurtosis	0.016
Angular range angular_range	— – 0.4700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	118800.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.627; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.380; Smooth: 0.973

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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	Env polyprotein (Fragment)
Molecular weight formula_weight	4515.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AaA
Atom count atom_count	1333

XNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQX

Entity 2 Entity 2 polymer

Description description	Transmembrane protein gp41
Molecular weight formula_weight	3792.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	BBB

QIWNNMTWMEWDREXNNYTSLIHSLIEESQ

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	87

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8. Citations (1)

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Unit-cell length a length_a	44.963 Å
Unit-cell length b length_b	44.963 Å
Unit-cell length c length_c	209.010 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	1.250 Å
Low-resolution limit resolution_low	38.280 Å
R factor r_factor	—
R_work r_work	0.1620
R_free r_free	0.2104

fit	/app/data/saxs_computation/tv/6tvu/6tvu.fit
pddf	/app/data/pr_computation/tv/6tvu/6tvu.pr.out
profile	/app/data/saxs_computation/tv/6tvu/6tvu.dat

Structure of native gp41 derived peptide fusion inhibitor

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

Env polyprotein (Fragment)

State in the Current Structure

Other States of the Same Protein in the Database

Transmembrane protein gp41

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)