4qdr

Physical basis for Nrp2 ligand binding

Method: X-RAY DIFFRACTION D_max: 78.7 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 276–595	Fragment：unp residues 276-595 Mutation：T319R	No other associated polymer	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

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 4QDR	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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 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 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
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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification 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 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 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 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 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
6TDB Neuropilin2-b1 domain in a complex with the C-terminal VEGFB167 peptide Deposited 2019-11-08	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 275–430（156 aa）	Not recorded	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
6TDB Neuropilin2-b1 domain in a complex with the C-terminal VEGFB167 peptide Deposited 2019-11-08	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 B 275–430（156 aa）	Not recorded	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
6TDB Neuropilin2-b1 domain in a complex with the C-terminal VEGFB167 peptide Deposited 2019-11-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 275–430（156 aa）	Not recorded	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
6TDB Neuropilin2-b1 domain in a complex with the C-terminal VEGFB167 peptide Deposited 2019-11-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 275–430（156 aa）	Not recorded	No recorded non-water small molecule	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
6TJT Neuropilin2-b1 domain in a complex with the C-terminal VEGFC peptide Deposited 2019-11-26	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 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 31 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 5–324； UniProt 276–595

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	4qdr
Deposition date deposition_date	2014-05-14
Structure title title	Physical basis for Nrp2 ligand binding
Keywords keywords	coagulation factor domain, discoidin domain, receptor, VEGF-C, membrane, CELL ADHESION; CELL ADHESION
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	22.94 Å
Radius of gyration Rg (electron density) rg_electron	22.04 Å
Forward intensity I(0) i0	22980900.00
Molecular weight molecular_weight	35654.0 kDa
Excluded volume excluded_volume	44271 Å³
Envelope volume envelope_volume	52381 Å³
Hydration-shell volume shell_volume	20718 Å³
Envelope diameter envelope_diameter	80.9 Å
Shell Rg shell_rg	27.87 Å
Envelope Rg envelope_rg	22.27 Å
Shape Rg shape_rg	22.09 Å
Total Rg total_rg	22.65 Å
Total atoms total_atoms	2513
Residues n_residues	314
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	78.7 Å
Rg (real space) rg_real	23.04 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	2.2980e+07
I(0) uncertainty (real space) i0_real_error	3.4730e+05
Rg (reciprocal space) rg_reciprocal	23.02 Å
I(0) (reciprocal space) i0_reciprocal	22980000.0000
Solution quality estimate total_estimate	0.8566
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	0.468
Kurtosis Kurtosis kurtosis	-0.316
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4609000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.756; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.908; Smooth: 0.957

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4qdra1
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.0 — automated matches

Domain ID domain_id	d4qdra2
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.0 — automated matches

Domain ID domain_id	d4qdra3
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 (2 domains)

Domain ID domain_id	4qdrA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	4qdrA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

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8. Citations (1)

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Unit-cell length a length_a	34.901 Å
Unit-cell length b length_b	70.759 Å
Unit-cell length c length_c	122.974 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	19.690 Å
R factor r_factor	0.2036
R_work r_work	0.2009
R_free r_free	0.2551

Description description	Neuropilin-2
Molecular weight formula_weight	36599.2 kDa
Mutation mutation	T319R
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2636

Physical basis for Nrp2 ligand binding

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	123

fit	/app/data/saxs_computation/qd/4qdr/4qdr.fit
pddf	/app/data/pr_computation/qd/4qdr/4qdr.pr.out
profile	/app/data/saxs_computation/qd/4qdr/4qdr.dat