MolNFT v1 · #136738 · protein

De novo design of novel covalent constrained meso-size peptide scaffolds with unique tertiary structures

5V2G · 20-mer peptide: “De novo design of novel covalent constrained meso-size peptide scaffolds with unique tertiary structures”. Solution nmr, 1 ligand (ZBR), 1 pocket (best druggability 0.45). MolNFT v1 #136738 on GenesisL1: 3D…

PDB: 5V2G
Type: protein
Length: 60 residues
Chains: 3
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 20-mer peptide
Ligands: ZBR
Pockets: 1 · best druggability 0.45

Structure

solution nmr · 1 distinct chain · 65% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	20-mer peptide	protein	20	65% helix, 0% strand	—

Ligands and binding sites

ZBR · 1,3,5-tris(bromomethyl)benzene · ligand · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	161	0.45	0.75	18	ZBR

Interfaces

3 interfaces between chains.

B–C · 255 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 251 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 251 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent (covalent ligand).

Compared structures

5V2G · De Novo Design of Novel Covalent Constrained Meso-size Peptide Scaffolds with Unique… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 5V2G · PDBe 5V2G

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