MolNFT v1 · #142612 · protein
Crystal structure of ICP55 from saccharomyces cerevisiae (N-terminal 42 residues deletion)
6A9V · Intermediate cleaving peptidase 55: “Crystal structure of ICP55 from saccharomyces cerevisiae (N-terminal 42 residues deletion)”. X-ray diffraction, 2 ligands (GLY, MN), 4 pockets (best druggability 0.51). MolNFT v1 #142612 on…
- PDB
- 6A9V
- Type
- protein
- Length
- 393 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, MN
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Intermediate cleaving peptidase 55 (EC 3.4.11.26) | protein | 393 | 39% helix, 21% strand | P40051 |
Ligands and binding sites
- GLY · Glycine · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.51 | 0.76 | 36 | PGE, GLY |
| 2 | 82 | 0.42 | 0.79 | 15 | empty |
| 3 | 61 | 0.32 | 0.76 | 21 | empty |
| 4 | 62 | 0.32 | 0.76 | 15 | empty |
Compared structures
- 6A9V · Crystal structure of Icp55 from Saccharomyces cerevisiae (N-terminal 42 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 6A9V · PDBe 6A9V · UniProt P40051
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