MolNFT v2 · #226601 · protein
Structure of the A type blood alpha-D-galactosamine galactosaminidase from Flavonifractor plautii in complex with GalN-pNP
9AWT: “Structure of the A type blood alpha-D-galactosamine galactosaminidase from Flavonifractor plautii in complex…”. X-ray diffraction at 2.3, 5 ligands (A1AHC, ZN, CO), 20 pockets (best druggability 0.81). MolNFT v2 #226601 on…
- PDB
- 9AWT
- Type
- protein
- Length
- 3,270 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Flavonifractor plautii
- Molecule
- A type blood alpha-D-galactosamine galactosaminidase
- EC
- 3.2.1.-
- UniProt
- P0DTR5
- Ligands
- A1AHC, ZN, CO, MN, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.3 · 1 distinct chain · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | A type blood alpha-D-galactosamine galactosaminidase (EC 3.2.1.-) | protein | 654 | 23% helix, 34% strand | P0DTR5 |
Ligands and binding sites
- A1AHC · 4-nitrophenyl 2-amino-2-deoxy-alpha-D-galactopyranoside · ligand · 5 copies · chains A, B, C, D, E
- ZN · Zinc ion · metal · 5 copies · chains A, B, C, D, E
- CO · Cobalt (II) ion · metal · 5 copies · chains A, B, C, D, E
- MN · Manganese (II) ion · metal · 5 copies · chains A, B, C, D, E
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.81 | 0.84 | 110 | A1AHC |
| 2 | 946 | 0.80 | 0.82 | 90 | A1AHC |
| 3 | 620 | 0.79 | 0.84 | 71 | A1AHC |
| 4 | 340 | 0.74 | 0.86 | 61 | empty |
| 5 | 365 | 0.70 | 0.83 | 57 | empty |
Interfaces
6 interfaces between chains.
- A–B · 692 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 682 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 548 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 280 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 211 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- P0DTR5 · AlphaFold monomer V2.0 prediction for a type blood alpha-D- galactosamine… · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P0DTR5
- Elsewhere: RCSB PDB 9AWT · PDBe 9AWT · UniProt P0DTR5
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