Research workbench
Crystal structure of spacer 8AA-shortened cephalosporin acylase mutant
Analyse Crystal structure of spacer 8AA-shortened cephalosporin acylase mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E56
- Type
- protein
- Length
- 1,328 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cephalosporin acylase
- EC
- 3.5.1.93
- UniProt
- O86089
- Ligands
- CA
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cephalosporin acylase (EC 3.5.1.93) | protein | 664 | 34% helix, 24% strand | O86089 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.82 | 0.83 | 99 | CA |
| 2 | 262 | 0.59 | 0.78 | 42 | empty |
| 3 | 239 | 0.58 | 0.79 | 37 | empty |
| 4 | 220 | 0.54 | 0.78 | 45 | empty |
| 5 | 229 | 0.53 | 0.77 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 829 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4E56 · Crystal Structure of spacer 8aa-shortened cephalosporin acylase mutant · the same entry in another collection · chain A against A, TM-score 1.00
- 1GK0 · Structure-based prediction of modifications in glutarylamidase to allow single-step… · a predicted model of the same protein · chain B against B, TM-score 0.78
- 1GK1 · Structure-based prediction of modifications in glutarylamidase to allow single-step… · a predicted model of the same protein · chain B against B, TM-score 0.78
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 O86089
- Elsewhere: RCSB PDB 4E56 · PDBe 4E56 · UniProt O86089
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