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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "nrp1"

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Search Summary

This query matches 32 Structures.

Refinements

Structure Determination Methodology

experimental (32)

Scientific Name of Source Organism

	Homo sapiens (25)
	Mus musculus (3)
	Arabidopsis thaliana (2)
	Rattus norvegicus (2)
	Leiurus quinquestriatus (1)
	Severe acute respiratory syndrome coronavirus 2 (1)
	synthetic construct (1)

Taxonomy

	Eukaryota (32)
	Riboviria (1)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (31)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

Protein (32)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (4)
	1.5 - 2.0 (11)
	2.0 - 2.5 (8)
	2.5 - 3.0 (5)
	3.0 - 3.5 (1)
	3.5 - 4.0 (1)
	> 4.5 (1)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (5)
	2010 - 2014 (4)
	2015 - 2019 (12)
	2020 - 2024 (10)

Symmetry Type

	Asymmetric (27)
	Cyclic (6)

SCOP Classification

	All beta proteins (16)
	Artifacts (11)
	All alpha proteins (1)
	Alpha and beta proteins (a+b) (2)

AllSelected

1 to 25 of 32 Structures

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1KEX \| pdb_00001kex	Download File View File

Crystal Structure of the b1 Domain of Human Neuropilin-1

Lee, C.C., Kreusch, A., McMullan, D., Ng, K., Spraggon, G.

(2003) Structure 11: 99-108

Released	2003-01-28
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Neuropilin-1 (protein)

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2ORX \| pdb_00002orx	Download File View File

Structural Basis for Ligand Binding and Heparin Mediated Activation of Neuropilin

Vander Kooi, C.W., Jusino, M.A., Perman, B., Neau, D.B., Bellamy, H.D., Leahy, D.J.

(2007) Proc Natl Acad Sci U S A 104: 6152-6157

Released	2007-04-03
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Rattus norvegicus
Macromolecule	Neuropilin-1 (protein)

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2ORZ \| pdb_00002orz	Download File View File

Structural Basis for Ligand Binding and Heparin Mediated Activation of Neuropilin

Vander Kooi, C.W., Jusino, M.A., Perman, B., Neau, D.B., Bellamy, H.D., Leahy, D.J.

(2007) Proc Natl Acad Sci U S A 104: 6152-6157

Released	2007-04-03
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Rattus norvegicus
Macromolecule	Neuropilin-1 (protein) Tuftsin (protein)

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2QQI \| pdb_00002qqi	Download File View File

Crystal Structure of the b1b2 Domains from Human Neuropilin-1

Appleton, B.A., Desmarais, W., Wiesmann, C.

(2007) EMBO J 26: 4902-4912

Released	2007-11-20
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Neuropilin-1 (protein)
Unique Ligands	GOL

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2QQM \| pdb_00002qqm	Download File View File

Crystal Structure of the a2b1b2 Domains from Human Neuropilin-1

Appleton, B.A., Wiesmann, C.

(2007) EMBO J 26: 4902-4912

Released	2007-11-20
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Neuropilin-1 (protein)
Unique Ligands	CA, EDO
Unique branched monosaccharides	FUC, NAG

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2QQN \| pdb_00002qqn	Download File View File

Neuropilin-1 b1 Domain in Complex with a VEGF-Blocking Fab

Appleton, B.A., Wiesmann, C.

(2007) EMBO J 26: 4902-4912

Released	2007-11-20
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Antibody heavy chain (protein) Antibody light chain (protein) Neuropilin-1 (protein)
Unique Ligands	EDO

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3I97 \| pdb_00003i97	Download File View File

B1 domain of human Neuropilin-1 bound with small molecule EG00229

Allerston, C.K., Djordjevic, S.

(2010) J Med Chem 53: 2215-2226

Released	2010-03-02
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens
Macromolecule	Neuropilin-1 (protein)
Unique Ligands	8DR, GOL

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4DEQ \| pdb_00004deq	Download File View File

Structure of the Neuropilin-1/VEGF-A complex

Vander Kooi, C.W.

(2012) J Biological Chem 287: 11082-11089

Released	2012-02-08
Method	X-RAY DIFFRACTION 2.649 Å
Organisms	Homo sapiens
Macromolecule	Neuropilin-1, Vascular endothelial growth factor A (protein)
Unique Ligands	PO4

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4GZ9 \| pdb_00004gz9	Download File View File

Mouse Neuropilin-1, extracellular domains 1-4 (a1a2b1b2)

Janssen, B.J.C., Malinauskas, T., Siebold, C., Jones, E.Y.

(2012) Nat Struct Mol Biol 19: 1293-1299

Released	2012-10-17
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Mus musculus
Macromolecule	Neuropilin-1 (protein)
Unique Ligands	CA, EDO, NAG, SO4
Unique branched monosaccharides	BMA, NAG

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4GZA \| pdb_00004gza	Download File View File

Complex of mouse Plexin A2 - Semaphorin 3A - Neuropilin-1

Janssen, B.J.C., Malinauskas, T., Siebold, C., Jones, E.Y.

(2012) Nat Struct Mol Biol 19: 1293-1299

Released	2012-10-17
Method	X-RAY DIFFRACTION 7 Å
Organisms	Mus musculus
Macromolecule	Neuropilin-1 (protein) Plexin-A2 (protein) Semaphorin-3A (protein)
Unique Ligands	CA

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4RN5 \| pdb_00004rn5	Download File View File

B1 domain of human Neuropilin-1 with acetate ion in a ligand-binding site

Allerston, C.K., Yelland, T.S., Jarvis, A., Jenkins, K., Winfield, N., Cheng, L., Jia, H., Zachary, I., Selwood, D.L., Djordjevic, S.

To be published

Released	2015-10-28
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Homo sapiens
Macromolecule	Neuropilin-1 (protein)
Unique Ligands	ACT, GOL, ZN

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5C7G \| pdb_00005c7g	Download File View File

Crystal Structure of the b1 Domain of Human Neuropilin-1 in complex with a bicine molecule

Didierjean, C., Jelsch, C.

To be published

Released	2016-07-06
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Homo sapiens
Macromolecule	Neuropilin-1 (protein)
Unique Ligands	BCN, NA

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5DAY \| pdb_00005day	Download File View File

The structure of NAP1-Related Protein(NRP1) in Arabidopsis

Zhu, Y., Rong, L., Yang, Y., Zhang, C., Feng, H.Y., Zheng, L.N., Shen, W.H., Ma, J.B., Dong, A.W.

To be published

Released	2016-09-21
Method	X-RAY DIFFRACTION 2.329 Å
Organisms	Arabidopsis thaliana
Macromolecule	NAP1-related protein 1 (protein)
Unique Ligands	CA

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5IJR \| pdb_00005ijr	Download File View File

X-ray structure of neuropilin-1 b1 domain complexed with Arg-1 ligand.

Fotinou, C., Rana, R., Djordjevic, S., Yelland, T.

(2018) FEBS J 285: 1290-1304

Released	2017-03-29
Method	X-RAY DIFFRACTION 1.52 Å
Organisms	Homo sapiens
Macromolecule	Neuropilin-1 (protein)
Unique Ligands	DMS, HRG

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5IYY \| pdb_00005iyy	Download File View File

X-ray structure of neuropilin-1 b1 domain complexed with Arg-4 ligand.

Fotinou, C., Rana, R., Djordjevic, S., Yelland, T.

(2018) FEBS J 285: 1290-1304

Released	2017-04-05
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Neuropilin-1 (protein)
Unique Ligands	R40

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5J1X \| pdb_00005j1x	Download File View File

X-ray structure of neuropilin-1 b1 domain complexed with Arg-5 ligand.

Fotinou, C., Rana, R., Djordjevic, S., Yelland, T.

(2018) FEBS J 285: 1290-1304

Released	2017-04-05
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	Neuropilin-1 (protein)
Unique Ligands	AR5, DMS

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5JGI \| pdb_00005jgi	Download File View File

X-ray structure of neuropilin-1 b1 domain complexed with M45 compound

Fotinou, C., Rana, R., Djordjevic, S., Yelland, T.

(2018) FEBS J 285: 1290-1304

Released	2017-05-10
Method	X-RAY DIFFRACTION 1.38 Å
Organisms	Homo sapiens
Macromolecule	Neuropilin-1 (protein)
Unique Ligands	AAG

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5JGQ \| pdb_00005jgq	Download File View File

X-ray structure of neuropilin-1 b1 domain complexed with Arg-7 ligand.

Fotinou, C., Rana, R., Djordjevic, S., Yelland, T.

(2018) FEBS J 285: 1290-1304

Released	2017-05-10
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Neuropilin-1 (protein)
Unique Ligands	6JY, DMS

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5JHK \| pdb_00005jhk	Download File View File

X-ray structure of neuropilin-1 b1 domain complexed with Arg-6 ligand.

Fotinou, C., Rana, R., Djordjevic, S., Yelland, T.

(2018) FEBS J 285: 1290-1304

Released	2017-05-24
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Neuropilin-1 (protein)
Unique Ligands	6K8

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5L73 \| pdb_00005l73	Download File View File

MAM domain of human neuropilin-1

Yelland, T., Djordjevic, S.

(2016) Structure 24: 2008-2015

Released	2016-10-26
Method	X-RAY DIFFRACTION 2.24 Å
Organisms	Homo sapiens
Macromolecule	Neuropilin-1 (protein)
Unique Ligands	BCN, CA, TAM

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6FMC \| pdb_00006fmc	Download File View File

Neuropilin1-b1 domain in complex with EG01377, 0.9 Angstrom structure

Yelland, T., Djordjevic, S., Fotinou, K., Selwood, D., Zachary, I., Frankel, P.

(2018) J Med Chem 61: 4135-4154

Released	2018-10-17
Method	X-RAY DIFFRACTION 0.9 Å
Organisms	Homo sapiens
Macromolecule	Neuropilin-1 (protein)
Unique Ligands	DUE

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6FMF \| pdb_00006fmf	Download File View File

Neuropilin-1 b1 domain in complex with EG01377; 2.8 Angstrom structure

Yelland, T., Djordjevic, S., Selwood, D., Zachary, I., Frankel, P.

(2018) J Med Chem 61: 4135-4154

Released	2018-10-17
Method	X-RAY DIFFRACTION 2.811 Å
Organisms	Homo sapiens
Macromolecule	Neuropilin-1 (protein)
Unique Ligands	DUE, TFA

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6POL \| pdb_00006pol	Download File View File

Crystal structure of the human NELL1 EGF1-3-Robo3 FN1 complex

Wang, J., Pak, J.S., Ozkan, E.

(2020) Nat Commun 11: 1489-1489

Released	2020-05-06
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Protein kinase C-binding protein NELL1 (protein) Roundabout homolog 3 (protein)
Unique Ligands	CA, GOL, NAG, NO3

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6TKK \| pdb_00006tkk	Download File View File

Neuropilin 1-b1 domain in a complex with the C-terminal VEGFB186 peptide

Eldrid, C., Yu, L., Yelland, T., Fotinou, C., Djordjevic, S.

To be published

Released	2020-12-16
Method	X-RAY DIFFRACTION 1.06 Å
Organisms	Homo sapiens
Macromolecule	ACE-ARG-PRO-GLN-PRO-ARG (protein) Neuropilin-1 (protein)
Unique Ligands	EDO

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7C7X \| pdb_00007c7x	Download File View File

Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1)

Luo, Q., Baihui, W.

(2020) Proc Natl Acad Sci U S A 117: 30391-30399

Released	2020-11-11
Method	X-RAY DIFFRACTION 3 Å
Organisms	Arabidopsis thaliana
Macromolecule	Histone H2A.6 (protein) Histone H2B.1 (protein) NAP1-related protein 1 (protein)
Unique Ligands	GOL

1 to 25 of 32 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Symmetry Type

SCOP Classification

1KEX | pdb_00001kex

2ORX | pdb_00002orx

2ORZ | pdb_00002orz

2QQI | pdb_00002qqi

2QQM | pdb_00002qqm

2QQN | pdb_00002qqn

3I97 | pdb_00003i97

4DEQ | pdb_00004deq

4GZ9 | pdb_00004gz9

4GZA | pdb_00004gza

4RN5 | pdb_00004rn5

5C7G | pdb_00005c7g

5DAY | pdb_00005day

5IJR | pdb_00005ijr

5IYY | pdb_00005iyy

5J1X | pdb_00005j1x

5JGI | pdb_00005jgi

5JGQ | pdb_00005jgq

5JHK | pdb_00005jhk

5L73 | pdb_00005l73

6FMC | pdb_00006fmc

6FMF | pdb_00006fmf

6POL | pdb_00006pol

6TKK | pdb_00006tkk

7C7X | pdb_00007c7x