Research workbench

Crystal structure of the dap bii hexapeptide complex I

Analyse Crystal structure of the dap bii hexapeptide complex I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WOO
Type: protein
Length: 1,404 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dipeptidyl aminopeptidase bii; Angiotensin II
EC: 3.4.14.-
UniProt: V5YM14
Ligands: ZN
Pockets: 13 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dipeptidyl aminopeptidase bii (EC 3.4.14.-)	protein	697	52% helix, 15% strand	V5YM14
C, D	Angiotensin II	protein	5	0% helix, 0% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B
GOL · Glycerol · additive · 12 copies · chains A, B

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

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	802	0.76	0.80	80	GOL
2	767	0.74	0.79	84	GOL
3	791	0.72	0.78	78	empty
4	674	0.70	0.78	88	empty
5	352	0.65	0.80	31	GOL

Interfaces

3 interfaces between chains.

B–D · 567 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 556 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 519 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3WOO · Crystal structure of the DAP BII hexapeptide complex I · 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 B 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 3WOO · PDBe 3WOO · UniProt V5YM14

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.