1z3u

Structure of the Angiopoietin-2 Recptor Binding Domain and Identification of Surfaces Involved in Tie2 Recognition

Method: X-RAY DIFFRACTION D_max: 185.9 Å Quality: REASONABLE

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 281–496	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 281–496	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 281–496	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 281–496	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

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 1Z3U	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 mutation/modification 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 mutation/modification 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
2GY7 Angiopoietin-2/Tie2 Complex Crystal Structure Deposited 2006-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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 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 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 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
8VGP CryoEM structure of Angiopoietin-2 in complex with engineered conformationally rigid Fab 5A12.6DS Deposited 2023-12-27	Different construct Different mutation/modification Different oligomeric state 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	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9HMI Crystal structure of the Calf domains of Integrin Alpha5 in complex with angiopoietin2 peptide Deposited 2024-12-09	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 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 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AGP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–217； UniProt 281–496 Author chain B； PDBConstruct 2–217； UniProt 281–496 Author chain C； PDBConstruct 2–217； UniProt 281–496 Author chain D； PDBConstruct 2–217； UniProt 281–496

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1z3u
Deposition date deposition_date	2005-03-14
Structure title title	Structure of the Angiopoietin-2 Recptor Binding Domain and Identification of Surfaces Involved in Tie2 Recognition
Keywords keywords	Tie2 binding, angiogenesis, extracellular ligand, SIGNALING PROTEIN; SIGNALING 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	61.86 Å
Radius of gyration Rg (electron density) rg_electron	61.19 Å
Forward intensity I(0) i0	143737000.00
Molecular weight molecular_weight	97781.0 kDa
Excluded volume excluded_volume	120710 Å³
Envelope volume envelope_volume	219390 Å³
Hydration-shell volume shell_volume	29774 Å³
Envelope diameter envelope_diameter	157.2 Å
Shell Rg shell_rg	69.89 Å
Envelope Rg envelope_rg	54.86 Å
Shape Rg shape_rg	61.19 Å
Total Rg total_rg	61.37 Å
Total atoms total_atoms	6880
Residues n_residues	864
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	185.9 Å
Rg (real space) rg_real	61.34 Å
Rg uncertainty (real space) rg_real_error	2.24 Å
I(0) (real space) i0_real	1.4370e+08
I(0) uncertainty (real space) i0_real_error	3.1780e+06
Rg (reciprocal space) rg_reciprocal	62.23 Å
I(0) (reciprocal space) i0_reciprocal	143900000.0000
Solution quality estimate total_estimate	0.6084
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	104.1 Å
Skewness Skewness skewness	-0.601
Kurtosis Kurtosis kurtosis	-1.016
Angular range angular_range	— – 0.1250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2510000.0000
Real-space data points n_real_points	26
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.001; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.915; Smooth: 0.000

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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	Angiopoietin-2
Molecular weight formula_weight	24597.4 kDa
Mutation mutation	F469A, Y475A, Y476A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7259

SFRDCAEVFKSGHTTNGIYTLTFPNSTEEIKAYCDMEAGGGGWTIIQRREDGSVDFQRTWKEYKVGFGNPSGEYWLGNEFVSQLTNQQRYVLKIHLKDWEGNEAYSLYEHFYLSSEELNYRIHLKGLTGTAGKISSISQPGNDFSTKDGDNDKCICKCSQMLTGGWWFDACGPSNLNGMYYPQRQNTNKANGIKWAAWKGSGYSLKATTMMIRPADF

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	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	379

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1z3ua1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.171 — Fibrinogen C-terminal domain-like
Superfamily Superfamily superfamily	d.171.1 — Fibrinogen C-terminal domain-like
Family Family family	d.171.1.0 — automated matches

Domain ID domain_id	d1z3ua2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1z3ub1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.171 — Fibrinogen C-terminal domain-like
Superfamily Superfamily superfamily	d.171.1 — Fibrinogen C-terminal domain-like
Family Family family	d.171.1.0 — automated matches

Domain ID domain_id	d1z3ub2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1z3uc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.171 — Fibrinogen C-terminal domain-like
Superfamily Superfamily superfamily	d.171.1 — Fibrinogen C-terminal domain-like
Family Family family	d.171.1.0 — automated matches

Domain ID domain_id	d1z3uc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1z3ud1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.171 — Fibrinogen C-terminal domain-like
Superfamily Superfamily superfamily	d.171.1 — Fibrinogen C-terminal domain-like
Family Family family	d.171.1.0 — automated matches

Domain ID domain_id	d1z3ud2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	1z3uA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

Domain ID domain_id	1z3uA02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
Homologous superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

Domain ID domain_id	1z3uB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

Domain ID domain_id	1z3uB02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
Homologous superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

Domain ID domain_id	1z3uC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

Domain ID domain_id	1z3uC02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
Homologous superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

Domain ID domain_id	1z3uD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

Domain ID domain_id	1z3uD02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
Homologous superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

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8. Citations (1)

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Unit-cell length a length_a	140.218 Å
Unit-cell length b length_b	94.468 Å
Unit-cell length c length_c	84.673 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.47 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2460
R_work r_work	0.2460
R_free r_free	0.2780

fit	/app/data/saxs_computation/z3/1z3u/1z3u.fit
pddf	/app/data/pr_computation/z3/1z3u/1z3u.pr.out
profile	/app/data/saxs_computation/z3/1z3u/1z3u.dat