MolNFT v1 · #37748 · protein

Native dpp-IV (CD26) from rat

2GBC · Dipeptidyl peptidase 4: “Native dpp-IV (CD26) from rat”. X-ray diffraction, 1 ligand (NAG), 12 pockets (best druggability 0.79). MolNFT v1 #37748 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2GBC
Type: protein
Length: 1,460 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dipeptidyl peptidase 4
EC: 3.4.15.5
UniProt: P14740
Ligands: NAG
Pockets: 12 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 19% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dipeptidyl peptidase 4 (EC 3.4.15.5)	protein	730	19% helix, 37% strand	P14740

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	153	0.79	0.95	29	empty
2	846	0.72	0.77	113	empty
3	707	0.68	0.76	88	empty
4	383	0.56	0.74	52	empty
5	274	0.50	0.74	41	empty

Interfaces

1 interface between chains.

A–B · 2248 Å² buried · 45 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 10 glycan (disulfide, N-glycosylation).

Compared structures

2GBC · Native DPP-IV (CD26) from Rat · the same entry in another collection · chain A against A, TM-score 1.00
P14740 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P14740) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P14740
Elsewhere: RCSB PDB 2GBC · PDBe 2GBC · UniProt P14740

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