Research workbench
Acetobacter turbidans alpha-amino acid ester hydrolase complexed with phenylglycine
Analyse Acetobacter turbidans alpha-amino acid ester hydrolase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B4K
- Type
- protein
- Length
- 2,468 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-amino acid ester hydrolase
- EC
- 3.1.1.43
- UniProt
- Q8VRK8
- Ligands
- PG9
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alpha-amino acid ester hydrolase (EC 3.1.1.43) | protein | 617 | 24% helix, 28% strand | Q8VRK8 |
Ligands and binding sites
- PG9 · D-phenylglycine · ligand · 3 copies · chains A, B, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.79 | 0.81 | 115 | empty |
| 2 | 974 | 0.79 | 0.81 | 85 | empty |
| 3 | 1170 | 0.76 | 0.79 | 91 | empty |
| 4 | 1200 | 0.76 | 0.79 | 93 | empty |
| 5 | 508 | 0.70 | 0.80 | 43 | PG9 |
Interfaces
6 interfaces between chains.
- A–C · 2306 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 2287 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1174 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1153 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 684 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2B4K · Acetobacter turbidans alpha-amino acid ester hydrolase complexed with phenylglycine · 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 Q8VRK8
- Elsewhere: RCSB PDB 2B4K · PDBe 2B4K · UniProt Q8VRK8
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