MolNFT v1 · #135445 · protein
Burkholderia sp. beta-aminopeptidase
5TZB · D-aminopeptidase: “Burkholderia sp. beta-aminopeptidase”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.86). MolNFT v1 #135445 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5TZB
- Type
- protein
- Length
- 2,834 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-aminopeptidase
- UniProt
- A0A0J6Q6M7
- Ligands
- CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-aminopeptidase | protein | 354 | 32% helix, 27% strand | A0A0J6Q6M7 |
| C, F, D | D-aminopeptidase | protein | 355 | 31% helix, 27% strand | A0A0J6Q6M7 |
| G, H | D-aminopeptidase | protein | 353 | 30% helix, 27% strand | A0A0J6Q6M7 |
| E | D-aminopeptidase | protein | 355 | 32% helix, 26% strand | A0A0J6Q6M7 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, C, B, D, G, H, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.86 | 0.87 | 141 | empty |
| 2 | 907 | 0.84 | 0.86 | 72 | empty |
| 3 | 921 | 0.84 | 0.86 | 69 | empty |
| 4 | 682 | 0.75 | 0.81 | 94 | empty |
| 5 | 713 | 0.74 | 0.80 | 87 | empty |
Interfaces
15 interfaces between chains.
- G–F · 1887 Ų buried · 41 hydrogen bonds · protein-protein
- A–D · 1887 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 1885 Ų buried · 42 hydrogen bonds · protein-protein
- E–H · 1880 Ų buried · 42 hydrogen bonds · protein-protein
- F–H · 1554 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5TZB · Burkholderia sp. beta-aminopeptidase · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0J6Q6M7
- Elsewhere: RCSB PDB 5TZB · PDBe 5TZB · UniProt A0A0J6Q6M7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.