Research workbench
2.75 ångström resolution crystal structure of acetamidase from yersinia enterocolitica.
Analyse 2.75 ångström resolution crystal structure of acetamidase from yersinia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UBU
- Type
- protein
- Length
- 1,320 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ACETAMIDASE/FORMAMIDASE
- UniProt
- A0A0H3NNJ4
- Ligands
- NA
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative ACETAMIDASE/FORMAMIDASE | protein | 330 | 15% helix, 37% strand | A0A0H3NNJ4 |
| B | Putative ACETAMIDASE/FORMAMIDASE | protein | 331 | 16% helix, 37% strand | A0A0H3NNJ4 |
| D | Putative ACETAMIDASE/FORMAMIDASE | protein | 329 | 16% helix, 37% strand | A0A0H3NNJ4 |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.81 | 0.82 | 109 | empty |
| 2 | 1112 | 0.81 | 0.82 | 99 | empty |
| 3 | 224 | 0.52 | 0.77 | 35 | empty |
| 4 | 245 | 0.51 | 0.75 | 38 | empty |
| 5 | 165 | 0.47 | 0.76 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2555 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2553 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 1466 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1458 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 589 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 modified (engineered).
Compared structures
- 5UBU · 2.75 Angstrom Resolution Crystal Structure of Acetamidase from Yersinia enterocolitica. · 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 A0A0H3NNJ4
- Elsewhere: RCSB PDB 5UBU · PDBe 5UBU · UniProt A0A0H3NNJ4
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