SAXSdb — 6mxs

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

anti-VEGF-A Fab fragment bH1 heavy chain

Homo sapiens

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 A； UniProt 130–246 Chain H； UniProt 130–246	Mutation：Y33W,D98F,G99M	anti-VEGF-A Fab fragment bH1 light chain × 2 （Q7Z3Y4） 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

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 6MXS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6MHG Cryo-EM structure of the circumsporozoite protein of Plasmodium falciparum with a vaccine-elicited antibody reveals maturation of inter-antibody contacts Deposited 2018-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric	Chain A 130–244（115 aa） Chain B 130–244（115 aa） Chain C 130–244（115 aa） Chain D 130–244（115 aa） Chain F 130–244（115 aa） Chain G 130–244（115 aa） Chain H 130–244（115 aa） Chain I 130–244（115 aa） Chain J 130–244（115 aa） Chain K 130–244（115 aa） Chain M 130–244（115 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.57 Å
6MXR Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M] Deposited 2018-10-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 130–246（117 aa） Chain H 130–246（117 aa）	Mutation：Y33W, D98M, G99M Mutation：Y33W, D98M, G99M	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
6MY4 Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M,LC-S30bR] Deposited 2018-11-01	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 130–246（117 aa） Chain H 130–246（117 aa）	Mutation：Y33W,D98M,G99M Mutation：Y33W,D98M,G99M	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 130–246（117 aa） Chain H 130–246（117 aa）	Mutation：Y33W,D98F,G99M Mutation：Y33W,D98F,G99M	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 130–247（118 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
7CZW S protein of SARS-CoV-2 in complex bound with P5A-2G7 Deposited 2020-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain H 127–470（344 aa） Chain J 127–470（344 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7CZY S protein of SARS-CoV-2 in complex bound with P5A-2F11_2B Deposited 2020-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain H 127–470（344 aa） Chain J 127–470（344 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7CZZ S protein of SARS-CoV-2 in complex bound with P5A-2F11_3B Deposited 2020-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric	Chain H 127–470（344 aa） Chain I 127–470（344 aa） Chain J 127–470（344 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7D03 S protein of SARS-CoV-2 in complex bound with FabP5A-2G7 Deposited 2020-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain H 126–470（345 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	V9HW68_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 110–226； UniProt 130–246 Author chain H； PDBConstruct 110–226； UniProt 130–246

anti-VEGF-A Fab fragment bH1 light chain

Homo sapiens

UniProt Q7Z3Y4

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 127–236 Chain L； UniProt 127–236	Not recorded	anti-VEGF-A Fab fragment bH1 heavy chain × 2 （V9HW68） 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

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 6MXS	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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification 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 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 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 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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
6MY4 Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M,LC-S30bR] Deposited 2018-11-01	Different mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 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 × 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 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 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 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 × 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 method 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
9MY8 D7 Herpes Virus Simplex Neutralizing Nanobody Bound to HSV Glycoprotein gD Deposited 2025-01-21	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 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	Resolution 2.30 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 B； PDBConstruct 109–218； UniProt 127–236 Author chain L； PDBConstruct 109–218； UniProt 127–236

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	6mxs
Deposition date deposition_date	2018-10-31
Structure title title	Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M]
Keywords keywords	Fab fragment, antibody assembly, aggregation, IMMUNE SYSTEM; IMMUNE SYSTEM
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	38.93 Å
Radius of gyration Rg (electron density) rg_electron	39.82 Å
Forward intensity I(0) i0	138680000.00
Molecular weight molecular_weight	94547.0 kDa
Excluded volume excluded_volume	117980 Å³
Envelope volume envelope_volume	157270 Å³
Hydration-shell volume shell_volume	37292 Å³
Envelope diameter envelope_diameter	146.3 Å
Shell Rg shell_rg	39.21 Å
Envelope Rg envelope_rg	40.35 Å
Shape Rg shape_rg	39.76 Å
Total Rg total_rg	40.00 Å
Total atoms total_atoms	6660
Residues n_residues	848
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	139.0 Å
Rg (real space) rg_real	39.80 Å
Rg uncertainty (real space) rg_real_error	1.83 Å
I(0) (real space) i0_real	1.3870e+08
I(0) uncertainty (real space) i0_real_error	2.4830e+06
Rg (reciprocal space) rg_reciprocal	39.26 Å
I(0) (reciprocal space) i0_reciprocal	138600000.0000
Solution quality estimate total_estimate	0.7326
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.9 Å
Skewness Skewness skewness	0.721
Kurtosis Kurtosis kurtosis	-0.091
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14340000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.521; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.507; Smooth: 0.450

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	anti-VEGF-A Fab fragment bH1 heavy chain
Molecular weight formula_weight	25438.5 kDa
Mutation mutation	Y33W,D98F,G99M
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,A
Atom count atom_count	7555

EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTWIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGFMFYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTGHHHHHHHHG

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	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	anti-VEGF-A Fab fragment bH1 light chain
Molecular weight formula_weight	23956.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,B

DIQMTQSPSSLSASVGDRVTITCRASQDIPRSISGYVAWYQQKPGKAPKLLIYWGSYLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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	Cricetulus griseus

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	844

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d6mxsa_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6mxsb1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6mxsb2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d6mxsh_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6mxsl1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6mxsl2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (6 domains)

Domain ID domain_id	6mxsA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6mxsB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6mxsB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6mxsH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6mxsL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6mxsL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	65.679 Å
Unit-cell length b length_b	95.960 Å
Unit-cell length c length_c	110.110 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.68 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1932
R_work r_work	0.1913
R_free r_free	0.2288

fit	/app/data/saxs_computation/mx/6mxs/6mxs.fit
pddf	/app/data/pr_computation/mx/6mxs/6mxs.pr.out
profile	/app/data/saxs_computation/mx/6mxs/6mxs.dat

Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M]

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

anti-VEGF-A Fab fragment bH1 heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

anti-VEGF-A Fab fragment bH1 light chain

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)