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2qqj

Crystal Structure of the b1b2 Domains from Human Neuropilin-2

Method: X-RAY DIFFRACTION Dmax: 78.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Neuropilin-2

Homo sapiens

UniProt O60462

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 275–595 Fragment：F5/8 type C 1 and C 2 domains 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

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 2QQJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 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 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 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 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 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 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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 275–429（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 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 275–429（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 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 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 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 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 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 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 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 275–430（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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 5–325； UniProt 275–595

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

SAXS profile for 2qqj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2qqj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2qqj
Deposition date deposition_date2007-07-26
Structure title titleCrystal Structure of the b1b2 Domains from Human Neuropilin-2
Keywords keywords;VEGF receptor, semaphorin receptor, Developmental protein, Differentiation, Glycoprotein, Membrane, Neurogenesis, Transmembrane, HORMONE, SIGNALING PROTEIN ;; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.00 Å
Radius of gyration Rg (electron density) rg_electron22.07 Å
Forward intensity I(0) i022889100.00
Molecular weight molecular_weight35604.0 kDa
Excluded volume excluded_volume44224 ų
Envelope volume envelope_volume52520 ų
Hydration-shell volume shell_volume20722 ų
Envelope diameter envelope_diameter81.6 Å
Shell Rg shell_rg27.90 Å
Envelope Rg envelope_rg22.29 Å
Shape Rg shape_rg22.11 Å
Total Rg total_rg22.70 Å
Total atoms total_atoms2509
Residues n_residues315
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax78.8 Å
Rg (real space) rg_real23.10 Å
Rg uncertainty (real space) rg_real_error0.56 Å
I(0) (real space) i0_real2.2890e+07
I(0) uncertainty (real space) i0_real_error3.1470e+05
Rg (reciprocal space) rg_reciprocal23.08 Å
I(0) (reciprocal space) i0_reciprocal22890000.0000
Solution quality estimate total_estimate0.8561
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.1 Å
Skewness Skewness skewness0.463
Kurtosis Kurtosis kurtosis-0.328
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4881000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.755; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.906; Smooth: 0.953
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2qqja1
Class classb — All beta proteins
Fold Fold foldb.18 — Galactose-binding domain-like
Superfamily Superfamily superfamilyb.18.1 — Galactose-binding domain-like
Family Family familyb.18.1.0 — automated matches
Domain ID domain_idd2qqja2
Class classb — All beta proteins
Fold Fold foldb.18 — Galactose-binding domain-like
Superfamily Superfamily superfamilyb.18.1 — Galactose-binding domain-like
Family Family familyb.18.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id2qqjA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id2qqjA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
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8. Citations (1)

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9. Files and Curves (10)