SAXSdb — 8vgp

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

Angiopoietin-2

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 225–444	Fragment：Receptor binding domain, UNP residues 225-444	Fab 5A12.6DS heavy chain × 1 Fab 5A12.6DS light chain × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.70 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 8VGP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Z3S Angiopoietin-2 Receptor Binding Domain Deposited 2005-03-14	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 281–496（216 aa） Fragment：Receptor binding domain (residues 281-496)	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG-4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.35 Å R-free 0.287
1Z3S Angiopoietin-2 Receptor Binding Domain Deposited 2005-03-14	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 281–496（216 aa） Fragment：Receptor binding domain (residues 281-496)	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG-4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.35 Å R-free 0.287
1Z3U Structure of the Angiopoietin-2 Recptor Binding Domain and Identification of Surfaces Involved in Tie2 Recognition Deposited 2005-03-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 281–496（216 aa） Fragment：Receptor binding domain (residues 281-496)	Mutation：F469A, Y475A, Y476A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；Ammonium Sulfate and PEG-4000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.25 Å R-free 0.278
1Z3U Structure of the Angiopoietin-2 Recptor Binding Domain and Identification of Surfaces Involved in Tie2 Recognition Deposited 2005-03-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 281–496（216 aa） Fragment：Receptor binding domain (residues 281-496)	Mutation：F469A, Y475A, Y476A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；Ammonium Sulfate and PEG-4000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.25 Å R-free 0.278
1Z3U Structure of the Angiopoietin-2 Recptor Binding Domain and Identification of Surfaces Involved in Tie2 Recognition Deposited 2005-03-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 281–496（216 aa） Fragment：Receptor binding domain (residues 281-496)	Mutation：F469A, Y475A, Y476A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；Ammonium Sulfate and PEG-4000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.25 Å R-free 0.278
1Z3U Structure of the Angiopoietin-2 Recptor Binding Domain and Identification of Surfaces Involved in Tie2 Recognition Deposited 2005-03-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 281–496（216 aa） Fragment：Receptor binding domain (residues 281-496)	Mutation：F469A, Y475A, Y476A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；Ammonium Sulfate and PEG-4000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.25 Å R-free 0.278
2GY7 Angiopoietin-2/Tie2 Complex Crystal Structure Deposited 2006-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 281–495（215 aa） Fragment：Angiopoietin-2 Receptor binding domain (residues 281-495)	Not recorded	CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；2.2 M Ammonium Sulfate, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.70 Å R-free 0.317
4JZC Angiopoietin-2 fibrinogen domain TAG mutant Deposited 2013-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 279–496（218 aa） Fragment：fibrinogen-like receptor-binding domain	Mutation：P183T, Q184A, R185G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.0 M Na/K-tartate, 0.1 M Tris, 0.2 M LiSO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.248
4JZC Angiopoietin-2 fibrinogen domain TAG mutant Deposited 2013-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 279–496（218 aa） Fragment：fibrinogen-like receptor-binding domain	Mutation：P183T, Q184A, R185G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.0 M Na/K-tartate, 0.1 M Tris, 0.2 M LiSO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.248
4ZFG Dual-specificity Fab 5A12 in complex with Angiopoietin 2 Deposited 2015-04-21	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 225–444（220 aa） Fragment：Receptor binding domain, UNP residues 225-444	Not recorded	CA CALCIUM ION × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；0.1 M Tris pH 8.5, 0.2 M lithium sulfate, 25% PEG 3350, 3% D(+)-sucrose	Resolution 2.27 Å R-free 0.223
9HMI Crystal structure of the Calf domains of Integrin Alpha5 in complex with angiopoietin2 peptide Deposited 2024-12-09	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 P 359–366（8 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium formate; 20% polyethylene glycol 3350 (wt/vol)	Resolution 2.78 Å R-free 0.306

6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ANGP2_HUMAN
Isoform	O15123-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–223； UniProt 225–444

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	8vgp
Deposition date deposition_date	2023-12-27
Structure title title	CryoEM structure of Angiopoietin-2 in complex with engineered conformationally rigid Fab 5A12.6DS
Keywords keywords	fab, antigen binding fragment, protein engineering, CYTOKINE-IMMUNE SYSTEM complex; CYTOKINE/IMMUNE SYSTEM
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	33.22 Å
Radius of gyration Rg (electron density) rg_electron	33.50 Å
Forward intensity I(0) i0	82084800.00
Molecular weight molecular_weight	70896.0 kDa
Excluded volume excluded_volume	88101 Å³
Envelope volume envelope_volume	112220 Å³
Hydration-shell volume shell_volume	31044 Å³
Envelope diameter envelope_diameter	122.6 Å
Shell Rg shell_rg	36.35 Å
Envelope Rg envelope_rg	33.47 Å
Shape Rg shape_rg	33.49 Å
Total Rg total_rg	33.76 Å
Total atoms total_atoms	4981
Residues n_residues	640
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	116.3 Å
Rg (real space) rg_real	33.77 Å
Rg uncertainty (real space) rg_real_error	1.10 Å
I(0) (real space) i0_real	8.2080e+07
I(0) uncertainty (real space) i0_real_error	1.3800e+06
Rg (reciprocal space) rg_reciprocal	33.54 Å
I(0) (reciprocal space) i0_reciprocal	82070000.0000
Solution quality estimate total_estimate	0.5701
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.1 Å
Skewness Skewness skewness	0.625
Kurtosis Kurtosis kurtosis	-0.221
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12190000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.675; Stabil: 1.000; Sysdev: 0.049; Positv: 1.000; Valcen: 0.579; Smooth: 0.657

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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	Angiopoietin-2
Molecular weight formula_weight	26530.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5046

AGSEQISFRDCAEVFKSGHTTNGIYTLTFPNSTEEIKAYCDMEAGGGGWTIIQRREDGSVDFQRTWKEYKVGFGNPSGEYWLGNEFVSQLTNQQRYVLKIHLKDWEGNEAYSLYEHFYLSSEELNYRIHLKGLTGTAGKISSISQPGNDFSTKDGDNDKCICKCSQMLTGGWWFDACGPSNLNGMYYPQRQNTNKFNGIKWYYWKGSGYSLKATTMMIRPADFGNSHHHHHH

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	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Fab 5A12.6DS heavy chain
Molecular weight formula_weight	25234.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQLVESGGGCVQPGGSLRLSCAASGFTISDYWIHWVRQAPGKGLEWVAGITPAGGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFVFFLPYAMDYWGQGTCVTVSSASTKGPSVCPLAPSSKSTSGGTACLGCLVKDYFCECPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTHHHHHHP

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 polymer

Description description	Fab 5A12.6DS light chain
Molecular weight formula_weight	23230.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIQMTQSPSSLSASVGDRVTITCRASQFLSSFGVAWYQQKCGKAPKLLIYGASSLYSGVPSRFSGSGSGTDFTLTISSLQCEDFATYYCQQGLLSPLTFGQGTKVEIKRTVAAPSVCIFPPSDECLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTCQDSKDCTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 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	43

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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	2.70 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	1017611

fit	/app/data/saxs_computation/vg/8vgp/8vgp.fit
pddf	/app/data/pr_computation/vg/8vgp/8vgp.pr.out
profile	/app/data/saxs_computation/vg/8vgp/8vgp.dat

CryoEM structure of Angiopoietin-2 in complex with engineered conformationally rigid Fab 5A12.6DS

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

Angiopoietin-2

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

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 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)