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Crystal structure of the DAP BII (G675R) dipeptide complex

Analyse Crystal structure of the DAP BII (G675R) dipeptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Y06
Type: protein
Length: 1,398 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.18
Source: Pseudoxanthomonas mexicana
Molecule: Dipeptidyl aminopeptidase BII
UniProt: V5YM14
Ligands: ZN
Pockets: 19 · best druggability 0.75

Structure

x-ray diffraction · resolution 2.18 · 1 distinct chain · 52% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dipeptidyl aminopeptidase BII	protein	699	52% helix, 15% strand	V5YM14

Ligands and binding sites

ZN · Zinc ion · metal · 5 copies · chains A, B
GOL · Glycerol · additive · 14 copies · chains A, B

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

Pockets

19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1100	0.75	0.78	119	GOL
2	700	0.71	0.78	84	empty
3	359	0.62	0.78	27	empty
4	305	0.61	0.79	37	GOL
5	350	0.61	0.78	32	empty

Interfaces

1 interface between chains.

A–B · 516 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4Y06 · Crystal structure of the dap bii (G675R) dipeptide complex · the same entry in another collection · chain A against A, TM-score 1.00
V5YM14 · AlphaFold monomer V2.0 prediction for dipeptidyl aminopeptidase bii (V5YM14) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 V5YM14
Elsewhere: RCSB PDB 4Y06 · PDBe 4Y06 · UniProt V5YM14

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