Research workbench
Crystal structure of ICP55 from saccharomyces cerevisiae (N-terminal 58 residues deletion)
Analyse Crystal structure of ICP55 from saccharomyces cerevisiae (N-terminal 58… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A9T
- Type
- protein
- Length
- 417 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intermediate cleaving peptidase 55
- EC
- 3.4.11.26
- UniProt
- P40051
- Ligands
- GLY, JEF, MN
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Intermediate cleaving peptidase 55 (EC 3.4.11.26) | protein | 417 | 39% helix, 19% strand | P40051 |
Ligands and binding sites
- GLY · Glycine · ligand · chains A
- JEF · O-(O-(2-aminopropyl)-O'-(2-methoxyethyl)polypropylene glycol 500) · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.59 | 0.78 | 47 | empty |
| 2 | 208 | 0.50 | 0.76 | 36 | GLY, JEF |
Compared structures
- 6A9T · Crystal structure of Icp55 from Saccharomyces cerevisiae (N-terminal 58 residues deletion) · the same entry in another collection · chain A against A, TM-score 1.00
- P40051 · AlphaFold monomer V2.0 prediction for intermediate cleaving peptidase 55 (P40051) · a predicted model of the same protein · 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 P40051
- Elsewhere: RCSB PDB 6A9T · PDBe 6A9T · UniProt P40051
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