MolNFT v1 · #142141 · protein

Structure of dipeptidyl-peptidase III from corallococcus sp. strain egb

5ZUM: “Structure of dipeptidyl-peptidase III from corallococcus sp. strain egb”. X-ray diffraction, 1 ligand (ZN), 15 pockets (best druggability 0.85). MolNFT v1 #142141 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZUM
Type: protein
Length: 1,070 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dipeptidyl-peptidase III
Ligands: ZN
Pockets: 15 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 55% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dipeptidyl-peptidase III	protein	533	55% helix, 14% strand	—
B	Dipeptidyl-peptidase III	protein	537	56% helix, 14% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	321	0.85	0.95	54	ZN
2	753	0.84	0.88	100	empty
3	230	0.83	0.96	38	empty
4	681	0.80	0.84	79	empty
5	282	0.72	0.86	28	empty

Interfaces

1 interface between chains.

A–B · 1450 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 modified (engineered).

Compared structures

5ZUM · Structure of dipeptidyl-peptidase III from Corallococcus sp. strain EGB · 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 5ZUM · PDBe 5ZUM

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