MolNFT v1 · #165125 · protein

Neuropilin 1-B1 domain in a complex with the C-terminal VEGFB186 peptide

6TKK · Neuropilin-1: “Neuropilin 1-B1 domain in a complex with the C-terminal VEGFB186 peptide”. X-ray diffraction, 1 ligand (ACE). MolNFT v1 #165125 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6TKK
Type: protein
Length: 163 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuropilin-1; ACE-arg-pro-gln-pro-arg
UniProt: O14786
Ligands: ACE

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neuropilin-1	protein	158	6% helix, 49% strand	O14786
B	ACE-arg-pro-gln-pro-arg	protein	5	0% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains B
EDO · 1,2-ethanediol · additive · 3 copies · chains A

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

Interfaces

1 interface between chains.

A–B · 326 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).

Compared structures

6TKK · Neuropilin 1-b1 domain in a complex with the C-terminal VEGFB186 peptide · the same entry in another collection · chain A against A, TM-score 1.00
O14786 · AlphaFold monomer V2.0 prediction for neuropilin-1 (O14786) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 O14786
Elsewhere: RCSB PDB 6TKK · PDBe 6TKK · UniProt O14786

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