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Crystal structure of the dap bii dipeptide complex II
Analyse Crystal structure of the dap bii dipeptide complex II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WOM
- 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
- 20 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl aminopeptidase bii (EC 3.4.14.-) | protein | 699 | 51% helix, 15% strand | V5YM14 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.63 | 0.80 | 29 | GOL |
| 2 | 335 | 0.63 | 0.79 | 51 | empty |
| 3 | 320 | 0.61 | 0.78 | 31 | empty |
| 4 | 167 | 0.60 | 0.83 | 21 | empty |
| 5 | 295 | 0.58 | 0.77 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 523 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 3WOM · PDBe 3WOM · UniProt V5YM14
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