MolNFT v1 · #4481 · protein

Dipeptide-binding protein

1DPE: “Dipeptide-binding protein”. X-ray diffraction, 1 ligand (CD), 6 pockets (best druggability 0.72). MolNFT v1 #4481 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1DPE
Type: protein
Length: 507 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dipeptide-binding protein
UniProt: P23847
Ligands: CD
Pockets: 6 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dipeptide-binding protein	protein	507	33% helix, 22% strand	P23847

Ligands and binding sites

CD · Cadmium ion · metal · 5 copies · chains A

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	609	0.72	0.80	68	empty
2	74	0.63	0.91	23	empty
3	91	0.46	0.81	19	empty
4	154	0.42	0.75	24	empty
5	79	0.35	0.76	18	empty

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

1DPE · Dipeptide-binding protein · the same entry in another collection · chain A against A, TM-score 1.00
P23847 · AlphaFold monomer V2.0 prediction for dipeptide-binding protein (P23847) · a predicted model of the same protein · chain A against A, TM-score 0.72

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 P23847
Elsewhere: RCSB PDB 1DPE · PDBe 1DPE · UniProt P23847

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