MolNFT v1 · #104537 · protein

Physical basis for NRP2 ligand binding

4QDR · Neuropilin-2: “Physical basis for NRP2 ligand binding”. X-ray diffraction, 2 pockets (best druggability 0.48). MolNFT v1 #104537 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4QDR
Type: protein
Length: 314 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuropilin-2
UniProt: O60462
Pockets: 2 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neuropilin-2	protein	314	5% helix, 48% strand	O60462

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	160	0.48	0.77	30	empty
2	86	0.41	0.78	14	empty

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4QDR · 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 A against A, TM-score 0.99

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 4QDR · PDBe 4QDR · UniProt O60462

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