MolNFT v1 · #104538 · protein

Physical basis for NRP2 ligand binding

4QDS · Neuropilin-2: “Physical basis for NRP2 ligand binding”. X-ray diffraction, 1 pocket (best druggability 0.70). MolNFT v1 #104538 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4QDS
Type: protein
Length: 361 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuropilin-2
UniProt: O60462
Pockets: 1 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neuropilin-2	protein	182	15% helix, 42% strand	O60462
B	Neuropilin-2	protein	179	15% helix, 43% strand	O60462

Ligands and binding sites

GOL · Glycerol · additive · chains A
ACT · Acetate ion · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	619	0.70	0.78	38	empty

Interfaces

1 interface between chains.

A–B · 1053 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

4QDS · Physical basis for Nrp2 ligand binding · the same entry in another collection · chain A against A, TM-score 1.00
O60462 · AlphaFold monomer V2.0 prediction for neuropilin-2 (O60462) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 O60462
Elsewhere: RCSB PDB 4QDS · PDBe 4QDS · UniProt O60462

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