Research workbench
Crystal structure of protein of unknown function (possible aminopeptidase) S2589 from shigella flexneri 2A str. 2457T
Analyse Crystal structure of protein of unknown function (possible aminopeptidase)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YLO
- Type
- protein
- Length
- 2,076 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein SF2450
- UniProt
- Q83K87
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Hypothetical protein SF2450 | protein | 346 | 29% helix, 28% strand | Q83K87 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.76 | 0.79 | 110 | ZN |
| 2 | 943 | 0.73 | 0.77 | 97 | ZN |
| 3 | 288 | 0.71 | 0.85 | 51 | empty |
| 4 | 251 | 0.70 | 0.85 | 44 | empty |
| 5 | 246 | 0.69 | 0.85 | 44 | empty |
Interfaces
7 interfaces between chains.
- A–E · 2064 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 1153 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 1150 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1135 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1119 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 modified (engineered).
Compared structures
- 1YLO · Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 from… · 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 Q83K87
- Elsewhere: RCSB PDB 1YLO · PDBe 1YLO · UniProt Q83K87
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