MolNFT v1 · #166624 · protein
Amidohydrolase 2 from bifidobacterium longum subsp. infantis
6UVZ: “Amidohydrolase 2 from bifidobacterium longum subsp. infantis”. X-ray diffraction, 17 pockets (best druggability 0.81). MolNFT v1 #166624 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6UVZ
- Type
- protein
- Length
- 1,248 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amidohydrolase 2
- UniProt
- B7GNK8
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amidohydrolase 2 | protein | 251 | 41% helix, 17% strand | B7GNK8 |
| B, C | Amidohydrolase 2 | protein | 250 | 41% helix, 18% strand | B7GNK8 |
| D | Amidohydrolase 2 | protein | 248 | 40% helix, 18% strand | B7GNK8 |
| E | Amidohydrolase 2 | protein | 249 | 43% helix, 18% strand | B7GNK8 |
Ligands and binding sites
- 2PE · Nonaethylene glycol · additive · 3 copies · chains A, B, C, D
- CIT · Citric acid · additive · 2 copies · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.81 | 0.89 | 40 | empty |
| 2 | 401 | 0.80 | 0.89 | 40 | empty |
| 3 | 337 | 0.55 | 0.75 | 42 | empty |
| 4 | 182 | 0.51 | 0.78 | 21 | empty |
| 5 | 195 | 0.50 | 0.77 | 23 | empty |
Interfaces
6 interfaces between chains.
- B–C · 996 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 525 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 444 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 435 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 414 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 6UVZ · Amidohydrolase 2 from Bifidobacterium longum subsp. infantis · 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 B7GNK8
- Elsewhere: RCSB PDB 6UVZ · PDBe 6UVZ · UniProt B7GNK8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.