SAXSdb — 9my8

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

Ig-like domain-containing protein

Lama glama

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain L； UniProt 23–236	Not recorded	Anti-Nb Fab Heavy chain × 1 D7 Neutralizing Nanobody against HSV Glycoprotein D × 1 Glycoprotein D × 1 （Q5ICU7）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.30 Å

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 9MY8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1L7I Crystal Structure of the anti-ErbB2 Fab2C4 Deposited 2002-03-15	Different construct 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 L 23–236（214 aa） Fragment：light chain (residues 1-214)	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；35%-45% saturated (NH4)2SO4, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.80 Å R-free 0.230
5VL7 PCSK9 complex with Fab33 Deposited 2017-04-25	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 127–236（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；potassium sodium phosphate	Resolution 3.50 Å R-free 0.245
5VR9 CH1/Ckappa Fab based on Matuzumab Deposited 2017-05-10	Different construct 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 130–235（106 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；294 K；see publication for details	Resolution 2.15 Å R-free 0.244
5VR9 CH1/Ckappa Fab based on Matuzumab Deposited 2017-05-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 130–235（106 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；294 K；see publication for details	Resolution 2.15 Å R-free 0.244
5VSI CH1/Ckappa Fab mutant 15.1 Deposited 2017-05-11	Different construct 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 L 130–235（106 aa）	Not recorded	SO4 SULFATE ION × 5 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；294 K；see publication	Resolution 1.51 Å R-free 0.227
6BGT Structure of Trastuzumab Fab mutant in complex with Her2 extracellular domain Deposited 2017-10-29	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 A 127–236（110 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；100 mM MES, pH 6.5, 18% PEG3350, 10% glycerol	Resolution 2.70 Å R-free 0.247
6MH2 Structure of Herceptin Fab without antigen Deposited 2018-09-17	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 127–236（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；200 mM ammonium acetate, 100 mM Bis-Tris, pH 5.5, 25% v/v PEG3350	Resolution 2.80 Å R-free 0.306
6MH2 Structure of Herceptin Fab without antigen Deposited 2018-09-17	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 127–236（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；200 mM ammonium acetate, 100 mM Bis-Tris, pH 5.5, 25% v/v PEG3350	Resolution 2.80 Å R-free 0.306
6MXR Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M] Deposited 2018-10-31	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 127–236（110 aa） Chain L 127–236（110 aa）	Not recorded	CL CHLORIDE ION × 2 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 5.6；295 K；0.1 M tris-sodium citrate, pH 5.6, 11% PEG4000, 8% isopropanol	Resolution 2.04 Å R-free 0.200
6MXS Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M] Deposited 2018-10-31	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 127–236（110 aa） Chain L 127–236（110 aa）	Not recorded	CL CHLORIDE ION × 2 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 5.6；295 K；0.1 M tri-sodium citrate, pH 5.6, 12% PEG4000, 10% isopropanol	Resolution 1.95 Å R-free 0.229
6MY4 Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M,LC-S30bR] Deposited 2018-11-01	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 127–236（110 aa） Chain L 127–236（110 aa）	Mutation：S30bR,S30bR Mutation：S30bR,S30bR	EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8；295 K；0.05 M imidazole, pH 8.0, 18% PEG6000	Resolution 1.69 Å R-free 0.230
6MY5 Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M,LC-S30bR] Deposited 2018-11-01	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 127–236（110 aa） Chain L 127–236（110 aa）	Mutation：S30bR,S30bR Mutation：S30bR,S30bR	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8；295 K；0.04 M imidazole, pH 8.0, 21% PEG6000	Resolution 1.73 Å R-free 0.229
6U1N GPCR-Beta arrestin structure in lipid bilayer Deposited 2019-08-16	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 127–236（110 aa）	Not recorded	2CU 3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1-yl)-2-oxoethoxy]thieno[2,3-b]pyridine-2-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7ZLG Cryo-EM structure of C-mannosyltransferase CeDPY19, in complex with acceptor peptide and bound to CMT2-Fab and anti-Fab nanobody Deposited 2022-04-15	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain L 23–236（214 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.72 Å
7ZLI Cryo-EM structure of C-mannosyltransferase CeDPY19, in complex with Dol25-P-Man and bound to CMT2-Fab and anti-Fab nanobody Deposited 2022-04-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 23–236（214 aa）	Not recorded	IZY Dolichol monophosphate beta-D-Mannose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.99 Å
7ZLJ Cryo-EM structure of C-mannosyltransferase CeDPY19, in ternary complex with Dol25-P-C-Man and acceptor peptide, bound to CMT2-Fab and anti-Fab nanobody Deposited 2022-04-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain L 23–236（214 aa）	Not recorded	IZU [(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl-[(3~{S},6~{E},10~{Z},14~{E})-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenoxy]phosphinic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.63 Å
9BDG Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with Fab ADI-85647 Deposited 2024-04-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric	Chain G 23–236（214 aa） Chain H 23–236（214 aa） Chain I 23–236（214 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å

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

View Construct and Data Evidence

UniProt name	Q7Z3Y4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–214； UniProt 23–236

Glycoprotein D

Human herpesvirus 2

UniProt Q5ICU7

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 26–330	Not recorded	Anti-Nb Fab Heavy chain × 1 Ig-like domain-containing protein × 1 （Q7Z3Y4） D7 Neutralizing Nanobody against HSV Glycoprotein D × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.30 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q5ICU7_HHV2
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–305； UniProt 26–330

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	9my8
Deposition date deposition_date	2025-01-21
最后修订 last_revision	2025-08-13
Structure title title	D7 Herpes Virus Simplex Neutralizing Nanobody Bound to HSV Glycoprotein gD
Keywords keywords	Neutralizing Antibody, ANTIVIRAL PROTEIN; ANTIVIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	34.92 Å
Radius of gyration Rg (electron density) rg_electron	34.90 Å
Forward intensity I(0) i0	109812000.00
Molecular weight molecular_weight	83922.0 kDa
Excluded volume excluded_volume	104950 Å³
Envelope volume envelope_volume	139770 Å³
Hydration-shell volume shell_volume	35335 Å³
Envelope diameter envelope_diameter	117.4 Å
Shell Rg shell_rg	39.20 Å
Envelope Rg envelope_rg	34.60 Å
Shape Rg shape_rg	34.85 Å
Total Rg total_rg	35.35 Å
Total atoms total_atoms	5914
Residues n_residues	771
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	117.0 Å
Rg (real space) rg_real	35.18 Å
Rg uncertainty (real space) rg_real_error	1.33 Å
I(0) (real space) i0_real	1.0980e+08
I(0) uncertainty (real space) i0_real_error	1.8070e+06
Rg (reciprocal space) rg_reciprocal	35.02 Å
I(0) (reciprocal space) i0_reciprocal	109800000.0000
Solution quality estimate total_estimate	0.8462
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	33.8 Å
Skewness Skewness skewness	0.473
Kurtosis Kurtosis kurtosis	-0.486
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13450000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.817; Smooth: 0.705

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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	Anti-Nb Fab Heavy chain
Molecular weight formula_weight	26328.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	7403

EVQLVESGGGLVQPGGSLRLSCAASGFNFSYYSIHWVRQAPGKGLEWVAYISSSSSYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARGYQYWQYHASWYWNGGLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTGSHHHHHH

来源 Source

来源生物 organism	Lama glama
通用名 common_name	llama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Ig-like domain-containing protein
Molecular weight formula_weight	23171.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSSLITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Lama glama
通用名 common_name	llama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	D7 Neutralizing Nanobody against HSV Glycoprotein D
Molecular weight formula_weight	13588.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

EVQLVESGGGLVQPGGSLRLSCSASGSIPSIWIMYWYRQAPGKGRELVAQITNFGTTVYADSVKGRFTISSDASKNTVYLQMNSLRAEDTAVYYCNLDVTLGPSRGAYWGKGTPVTVSSHHHHHH

来源 Source

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	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Glycoprotein D
Molecular weight formula_weight	36577.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

KYALADPSLKMADPNRFRGKNLPVLDQLTDPPGVKRVYHIQPSLEDPFQPPSIPITVYYAVLERACRSVLLHAPSEAPQIVRGASDEARKHTYNLTIAWYRMGDNCAIPITVMEYTECPYNKSLGVCPIRTQPRWSYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRARASCKYALPLRIPPAACLTSKAYQQGVTVDSIGMLPRFIPENQRTVALYSLKIAGWHGPKPPYTSTLLPPELSDTTNATQPELVPEDPEDSALLEDPAGTVSSQIPPNWHIPSIQDVAPHGGGSHHHHHHHHGSDYKDDDDK

来源 Source

来源生物 organism	Human herpesvirus 2
通用名 common_name	HHV-2, Human herpes simplex virus 2
NCBI Class编号 ncbi_taxonomy_id	10310
宿主生物 host_organism	Homo sapiens

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1489

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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	—

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.30 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	228770

fit	/app/data/saxs_computation/my/9my8/9my8.fit
pddf	/app/data/pr_computation/my/9my8/9my8.pr.out
profile	/app/data/saxs_computation/my/9my8/9my8.dat

D7 Herpes Virus Simplex Neutralizing Nanobody Bound to HSV Glycoprotein gD

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

Ig-like domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

Glycoprotein D

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)