MolNFT v1 · #110542 · protein

Crystal structure of dipeptidyl peptidase 11 (DPP11) from porphyromonas gingivalis

4Y01 · Peptidase S46: “Crystal structure of dipeptidyl peptidase 11 (DPP11) from porphyromonas gingivalis”. X-ray diffraction, 11 pockets (best druggability 0.72). MolNFT v1 #110542 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4Y01
Type: protein
Length: 1,398 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidase S46
UniProt: A0A076NW73
Pockets: 11 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Peptidase S46	protein	699	51% helix, 16% strand	A0A076NW73

Ligands and binding sites

GOL · Glycerol · additive · chains A

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

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	846	0.72	0.77	83	empty
2	627	0.67	0.76	55	GOL
3	260	0.56	0.77	27	empty
4	410	0.55	0.73	62	empty
5	132	0.39	0.74	19	empty

Interfaces

1 interface between chains.

A–B · 811 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 46 modified, 2 disulfide (engineered, disulfide).

Compared structures

4Y01 · Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis · 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
Every structure of UniProt A0A076NW73
Elsewhere: RCSB PDB 4Y01 · PDBe 4Y01 · UniProt A0A076NW73

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