6tdb

Neuropilin2-b1 domain in a complex with the C-terminal VEGFB167 peptide

Method: X-RAY DIFFRACTION D_max: 101.1 Å Quality: GOOD

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

Neuropilin-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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 275–430	Not recorded	C-terminal VEGFB167 peptide × 1 EDO 1,2-ETHANEDIOL × 1 ACE ACETYL GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；N2b1-apo 0.05 M KCl, 0.01 M MgCl2 and 15 % (w/v) PEG600 N2b1/VEGFB167 0.1 M HEPES pH 7.5, 10 % (w/v) PEG4000, 20 % (w/v) isopropanol	Resolution 2.45 Å R-free 0.250
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 275–430	Not recorded	C-terminal VEGFB167 peptide × 1 EDO 1,2-ETHANEDIOL × 1 ACE ACETYL GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；N2b1-apo 0.05 M KCl, 0.01 M MgCl2 and 15 % (w/v) PEG600 N2b1/VEGFB167 0.1 M HEPES pH 7.5, 10 % (w/v) PEG4000, 20 % (w/v) isopropanol	Resolution 2.45 Å R-free 0.250
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 275–430	Not recorded	C-terminal VEGFB167 peptide × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；N2b1-apo 0.05 M KCl, 0.01 M MgCl2 and 15 % (w/v) PEG600 N2b1/VEGFB167 0.1 M HEPES pH 7.5, 10 % (w/v) PEG4000, 20 % (w/v) isopropanol	Resolution 2.45 Å R-free 0.250
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 275–430	Not recorded	C-terminal VEGFB167 peptide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；N2b1-apo 0.05 M KCl, 0.01 M MgCl2 and 15 % (w/v) PEG600 N2b1/VEGFB167 0.1 M HEPES pH 7.5, 10 % (w/v) PEG4000, 20 % (w/v) isopropanol	Resolution 2.45 Å R-free 0.250

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 6TDB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2QQJ Crystal Structure of the b1b2 Domains from Human Neuropilin-2 Deposited 2007-07-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 275–595（321 aa） Fragment：F5/8 type C 1 and C 2 domains	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；297 K；0.1 M Bis-Tris, 20% PEG 5000 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 1.95 Å R-free 0.235
2QQK Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab Deposited 2007-07-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 23–595（573 aa） Fragment：CUB 1, CUB2, F5/8 type C 1, and C2 domains	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；297 K；0.1 M Hepes, 22% polyacrylic acid 5100, 0.02 M MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 2.75 Å R-free 0.243
2QQK Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab Deposited 2007-07-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 23–595（573 aa） Fragment：CUB 1, CUB2, F5/8 type C 1, and C2 domains	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；297 K；0.1 M Hepes, 22% polyacrylic acid 5100, 0.02 M MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 2.75 Å R-free 0.243
2QQL Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab Deposited 2007-07-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 23–595（573 aa） Fragment：CUB 1, CUB2, F5/8 type C 1, and C2 domains	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；10% PEG 1000, 10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 3.10 Å R-free 0.232
2QQL Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab Deposited 2007-07-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 23–595（573 aa） Fragment：CUB 1, CUB2, F5/8 type C 1, and C2 domains	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；10% PEG 1000, 10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 3.10 Å R-free 0.232
2QQO Crystal Structure of the a2b1b2 Domains from Human Neuropilin-2 Deposited 2007-07-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 145–595（451 aa） Fragment：CUB 2, F5/8 type C 1, and F5/8 type C 2 domains	Not recorded	CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；297 K；0.1 M Hepes, 10% PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 2.30 Å R-free 0.239
2QQO Crystal Structure of the a2b1b2 Domains from Human Neuropilin-2 Deposited 2007-07-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 145–595（451 aa） Fragment：CUB 2, F5/8 type C 1, and F5/8 type C 2 domains	Not recorded	CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；297 K；0.1 M Hepes, 10% PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 2.30 Å R-free 0.239
2QQO Crystal Structure of the a2b1b2 Domains from Human Neuropilin-2 Deposited 2007-07-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 145–595（451 aa） Fragment：CUB 2, F5/8 type C 1, and F5/8 type C 2 domains Chain B 145–595（451 aa） Fragment：CUB 2, F5/8 type C 1, and F5/8 type C 2 domains	Not recorded	CA CALCIUM ION × 2 EDO 1,2-ETHANEDIOL × 6 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；297 K；0.1 M Hepes, 10% PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 2.30 Å R-free 0.239
4QDQ Physical basis for Nrp2 ligand binding Deposited 2014-05-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 276–595（320 aa） Fragment：Neuropilin-2 b1b2 domain, VEGF-C C-terminus	Not recorded	GOL GLYCEROL × 6 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M HEPES, 0.5 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.95 Å R-free 0.241
4QDQ Physical basis for Nrp2 ligand binding Deposited 2014-05-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 276–595（320 aa） Fragment：Neuropilin-2 b1b2 domain, VEGF-C C-terminus	Not recorded	GOL GLYCEROL × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M HEPES, 0.5 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.95 Å R-free 0.241
4QDR Physical basis for Nrp2 ligand binding Deposited 2014-05-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 276–595（320 aa） Fragment：unp residues 276-595	Mutation：T319R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M HEPES, 18% (w/v) PEG 12000, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.255
4QDS Physical basis for Nrp2 ligand binding Deposited 2014-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 275–457（183 aa） Fragment：Proteolytic fragment of s9Nrp2 coagulation factor domains Chain B 275–457（183 aa） Fragment：Proteolytic fragment of s9Nrp2 coagulation factor domains	Not recorded	GOL GLYCEROL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；10% PEG 1000, 10% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.264
5DN2 Human NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A Deposited 2015-09-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 275–429（155 aa） Fragment：Neuropilin-2 domain B1 F5/8 type C 1, UNP residues 275-429	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；289 K；10% PEG20000, 0.1M Bicine, 2% v/v dioxane	Resolution 1.95 Å R-free 0.234
5DN2 Human NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A Deposited 2015-09-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 275–429（155 aa） Fragment：Neuropilin-2 domain B1 F5/8 type C 1, UNP residues 275-429	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；289 K；10% PEG20000, 0.1M Bicine, 2% v/v dioxane	Resolution 1.95 Å R-free 0.234
5DN2 Human NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A Deposited 2015-09-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 275–429（155 aa） Fragment：Neuropilin-2 domain B1 F5/8 type C 1, UNP residues 275-429	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；289 K；10% PEG20000, 0.1M Bicine, 2% v/v dioxane	Resolution 1.95 Å R-free 0.234
5DN2 Human NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A Deposited 2015-09-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 275–429（155 aa） Fragment：Neuropilin-2 domain B1 F5/8 type C 1, UNP residues 275-429	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；289 K；10% PEG20000, 0.1M Bicine, 2% v/v dioxane	Resolution 1.95 Å R-free 0.234
5DQ0 Structure of human neuropilin-2 b1 domain with novel and unique zinc binding site Deposited 2015-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 275–430（156 aa） Fragment：b1 domain, UNP residues 475-430	Not recorded	ZN ZINC ION × 3 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289.15 K；25 % PEG 550 MME, 0.1 M MES pH 6.5, 0.01 M ZnSO4	Resolution 1.80 Å R-free 0.217
6GH8 Crystal structure of GP1 domain of Lujo virus in complex with the first CUB domain of neuropilin-2 Deposited 2018-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 27–146（120 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.03M glycyl-glycyl-glycine, 25.9% PEG 6000, 0.09M Bis-Tris Propane pH 9.5	Resolution 2.44 Å R-free 0.311
6GH8 Crystal structure of GP1 domain of Lujo virus in complex with the first CUB domain of neuropilin-2 Deposited 2018-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 27–146（120 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.03M glycyl-glycyl-glycine, 25.9% PEG 6000, 0.09M Bis-Tris Propane pH 9.5	Resolution 2.44 Å R-free 0.311
6TJT Neuropilin2-b1 domain in a complex with the C-terminal VEGFC peptide Deposited 2019-11-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 275–430（156 aa）	Not recorded	SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M NaOAc, 0.1 M HEPES pH 7.5, 12 % (w/v) PEG4000	Resolution 1.31 Å R-free 0.179
6TJT Neuropilin2-b1 domain in a complex with the C-terminal VEGFC peptide Deposited 2019-11-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 275–430（156 aa）	Not recorded	SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M NaOAc, 0.1 M HEPES pH 7.5, 12 % (w/v) PEG4000	Resolution 1.31 Å R-free 0.179
7M22 Cryo-EM structure of the HCMV pentamer bound by human neuropilin 2 Deposited 2021-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain N 23–595（573 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Grid was blotted with a force of -6 for 3 seconds	Resolution 3.65 Å
7T4S CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with NRP2 and neutralizing fabs 8I21 and 13H11 Deposited 2021-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain F 1–864（864 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 3.5 seconds before plunging	Resolution 3.10 Å
8IVW Crystal structure of NRP2 in complex with aNRP2-10 Fab fragment Deposited 2023-03-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–595（571 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；21% PEG1000, 0.1M Sodium citrate tribasic dihydrate pH 5.5, 0.05M Lithium sulfate monohydrate	Resolution 3.21 Å R-free 0.294
8IVW Crystal structure of NRP2 in complex with aNRP2-10 Fab fragment Deposited 2023-03-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 25–595（571 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；21% PEG1000, 0.1M Sodium citrate tribasic dihydrate pH 5.5, 0.05M Lithium sulfate monohydrate	Resolution 3.21 Å R-free 0.294
8IVW Crystal structure of NRP2 in complex with aNRP2-10 Fab fragment Deposited 2023-03-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 25–595（571 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；21% PEG1000, 0.1M Sodium citrate tribasic dihydrate pH 5.5, 0.05M Lithium sulfate monohydrate	Resolution 3.21 Å R-free 0.294
8IVW Crystal structure of NRP2 in complex with aNRP2-10 Fab fragment Deposited 2023-03-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 25–595（571 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；21% PEG1000, 0.1M Sodium citrate tribasic dihydrate pH 5.5, 0.05M Lithium sulfate monohydrate	Resolution 3.21 Å R-free 0.294
8IVX Crystal structure of NRP2 in complex with aNRP2-14 Fab fragment Deposited 2023-03-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–595（571 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；289 K；30% PEG300, 0.1M Sodium acetate trihydrate pH 4.5	Resolution 1.90 Å R-free 0.225

15 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NRP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–159； UniProt 275–430 Author chain B； PDBConstruct 4–159； UniProt 275–430 Author chain C； PDBConstruct 4–159； UniProt 275–430 Author chain D； PDBConstruct 4–159； UniProt 275–430

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	6tdb
Deposition date deposition_date	2019-11-08
Structure title title	Neuropilin2-b1 domain in a complex with the C-terminal VEGFB167 peptide
Keywords keywords	VEGF-binding, NRP2, angiogenesis, immunomodulation, 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	30.18 Å
Radius of gyration Rg (electron density) rg_electron	29.64 Å
Forward intensity I(0) i0	92358900.00
Molecular weight molecular_weight	72914.0 kDa
Excluded volume excluded_volume	90080 Å³
Envelope volume envelope_volume	116750 Å³
Hydration-shell volume shell_volume	33001 Å³
Envelope diameter envelope_diameter	111.8 Å
Shell Rg shell_rg	36.28 Å
Envelope Rg envelope_rg	29.57 Å
Shape Rg shape_rg	29.58 Å
Total Rg total_rg	30.44 Å
Total atoms total_atoms	5154
Residues n_residues	641
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	101.1 Å
Rg (real space) rg_real	30.07 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	9.2360e+07
I(0) uncertainty (real space) i0_real_error	1.5280e+06
Rg (reciprocal space) rg_reciprocal	30.12 Å
I(0) (reciprocal space) i0_reciprocal	92360000.0000
Solution quality estimate total_estimate	0.8059
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	42.0 Å
Skewness Skewness skewness	0.141
Kurtosis Kurtosis kurtosis	-0.477
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24270000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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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	Neuropilin-2
Molecular weight formula_weight	18368.6 kDa
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	5469

GHMFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTSGS

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 polymer

Description description	C-terminal VEGFB167 peptide
Molecular weight formula_weight	731.9 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,J,K

RKLRR

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	ACETYL GROUP
Molecular weight formula_weight	44.1 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	277

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8. Citations (2)

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Unit-cell length a length_a	107.359 Å
Unit-cell length b length_b	140.122 Å
Unit-cell length c length_c	74.357 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	132.97 °
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	monoclinic

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	70.060 Å
R factor r_factor	0.1859
R_work r_work	0.1827
R_free r_free	0.2497

fit	/app/data/saxs_computation/td/6tdb/6tdb.fit
pddf	/app/data/pr_computation/td/6tdb/6tdb.pr.out
profile	/app/data/saxs_computation/td/6tdb/6tdb.dat

Neuropilin2-b1 domain in a complex with the C-terminal VEGFB167 peptide

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

Neuropilin-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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)