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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：O60462 New Search
16PDB entries
32Biological assembly
34chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
2QQJ Crystal Structure of the b1b2 Domains from Human Neuropilin-2 Deposited 2007-07-26 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
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 Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
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 Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.