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Crystal structure of the dap bii dipeptide complex III
Analyse Crystal structure of the dap bii dipeptide complex III in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WON
- Type
- protein
- Length
- 1,398 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl aminopeptidase bii
- EC
- 3.4.14.-
- UniProt
- V5YM14
- Ligands
- ZN
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl aminopeptidase bii (EC 3.4.14.-) | protein | 699 | 52% helix, 15% strand | V5YM14 |
Ligands and binding sites
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.73 | 0.79 | 92 | GOL |
| 2 | 656 | 0.72 | 0.79 | 87 | GOL |
| 3 | 538 | 0.65 | 0.76 | 57 | empty |
| 4 | 323 | 0.62 | 0.79 | 29 | empty |
| 5 | 296 | 0.59 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 516 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 3WON · PDBe 3WON · UniProt V5YM14
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