MolNFT v1 · #83639 · protein

Crystal structure of the dap bii hexapeptide complex II

3WOP · Dipeptidyl aminopeptidase bii: “Crystal structure of the dap bii hexapeptide complex II”. X-ray diffraction, 1 ligand (ZN), 17 pockets (best druggability 0.76). MolNFT v1 #83639 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3WOP
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 IV
EC: 3.4.14.-
UniProt: V5YM14
Ligands: ZN
Pockets: 17 · 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 IV	protein	5	0% helix, 0% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B
GOL · Glycerol · additive · 9 copies · chains A, B

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

Pockets

17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	898	0.76	0.79	98	GOL
2	773	0.74	0.79	80	empty
3	656	0.69	0.77	62	empty
4	616	0.67	0.76	60	empty
5	362	0.65	0.79	29	GOL

Interfaces

3 interfaces between chains.

A–C · 582 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 564 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 514 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3WOP · Crystal structure of the DAP BII hexapeptide complex II · 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 3WOP · PDBe 3WOP · UniProt V5YM14

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