MolNFT v1 · #47220 · protein

Structural basis for ligand binding and heparin mediated activation of neuropilin

2ORZ · Neuropilin-1: “Structural basis for ligand binding and heparin mediated activation of neuropilin”. X-ray diffraction, 2 pockets (best druggability 0.48). MolNFT v1 #47220 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2ORZ
Type: protein
Length: 316 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuropilin-1; Tuftsin
UniProt: Q9QWJ9
Pockets: 2 · best druggability 0.48

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neuropilin-1	protein	313	6% helix, 50% strand	Q9QWJ9
B	Tuftsin	protein	3	0% helix, 0% strand	—

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	186	0.48	0.75	28	empty
2	118	0.42	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 282 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

2ORZ · Structural Basis for Ligand Binding and Heparin Mediated Activation of Neuropilin · the same entry in another collection · chain A against A, TM-score 1.00
Q9QWJ9 · AlphaFold monomer V2.0 prediction for neuropilin-1 (Q9QWJ9) · a predicted model of the same protein · chain A against A, TM-score 0.96

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9QWJ9
Elsewhere: RCSB PDB 2ORZ · PDBe 2ORZ · UniProt Q9QWJ9

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