Research workbench
Structure of L-aminopeptidase D-ala-ESTERASE/AMIDASE from ochrobactrum anthropi, a prototype for the serine aminopeptidases, reveals a new variant among the ntn hydrolase fold
Analyse Structure of L-aminopeptidase D-ala-ESTERASE/AMIDASE from ochrobactrum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B65
- Type
- protein
- Length
- 2,178 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (aminopeptidase)
- UniProt
- Q59632
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Protein (aminopeptidase) | protein | 363 | 31% helix, 26% strand | Q59632 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.86 | 0.89 | 65 | empty |
| 2 | 590 | 0.79 | 0.85 | 50 | empty |
| 3 | 630 | 0.78 | 0.83 | 57 | empty |
| 4 | 599 | 0.78 | 0.84 | 59 | empty |
| 5 | 615 | 0.77 | 0.83 | 55 | empty |
Interfaces
8 interfaces between chains.
- A–D · 2228 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2224 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1378 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1374 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1329 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1B65 · Structure of l-aminopeptidase d-ala-esterase/amidase from ochrobactrum anthropi, a… · 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 Q59632
- Elsewhere: RCSB PDB 1B65 · PDBe 1B65 · UniProt Q59632
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