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Crystal structure of human dpp-IV in complex with HL2

Analyse Crystal structure of human dpp-IV in complex with HL2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZID
Type: protein
Length: 1,454 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dipeptidyl peptidase 4
EC: 3.4.14.5
UniProt: P27487
Ligands: 9EL, NAG, MAN
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dipeptidyl peptidase 4 (EC 3.4.14.5)	protein	727	18% helix, 37% strand	P27487

Ligands and binding sites

9EL · (2S,3R)-2-amino-9-methoxy-3-(2,4,5-trifluorophenyl)-2, 3-dihydro-1H-naphtho[2,1-b]pyran-8-carbonitrile · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, A
MAN · alpha-D-mannopyranose · sugar · 3 copies · chains B

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

Pockets

20 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	102	0.78	0.97	26	empty
2	853	0.71	0.76	99	9EL
3	481	0.66	0.78	62	9EL
4	276	0.58	0.78	51	empty
5	249	0.53	0.76	33	empty

Interfaces

1 interface between chains.

A–B · 2257 Å² buried · 39 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

5ZID · Crystal Structure of human DPP-IV in complex with HL2 · the same entry in another collection · chain A against A, TM-score 1.00
P27487 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P27487) · a predicted model of the same protein · chain A 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 P27487
Elsewhere: RCSB PDB 5ZID · PDBe 5ZID · UniProt P27487

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