MolNFT v2 · #117039 · protein

Human NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A

5DN2: “Human NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A”. X-ray diffraction at 1.95. MolNFT v2 #117039 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DN2
Type: protein
Length: 640 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.95
Source: Homo sapiens
UniProt: O60462, P15692

Structure

x-ray diffraction · resolution 1.95 · 3 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	—	protein	156	—	O60462
F, G	—	protein	4	—	P15692
E	—	protein	8	—	P15692

Ligands and binding sites

DIO · 1,4-diethylene dioxide · additive · 2 copies · chains B, D
GOL · Glycerol · additive · chains B

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

Compared structures

5DN2 · Human NRP2 B1 domain in complex with the peptide corresponding to the C-terminus of VEGF-a · the same entry in another collection · chain G against G, 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
P15692 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor a (P15692) · a predicted model of the same protein · chain F against A, TM-score 0.93

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
Every structure of UniProt P15692
Elsewhere: RCSB PDB 5DN2 · PDBe 5DN2 · UniProt O60462 · UniProt P15692

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.