Research workbench
Crystal strcture of ICP55 from saccharomyces cerevisiae bound to apstatin inhibitor
Analyse Crystal strcture of ICP55 from saccharomyces cerevisiae bound to apstatin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A9U
- Type
- protein
- Length
- 408 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intermediate cleaving peptidase 55; Apstatin
- EC
- 3.4.11.26
- UniProt
- P40051
- Ligands
- 01B, MN, NH2
- Pockets
- 6 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Intermediate cleaving peptidase 55 (EC 3.4.11.26) | protein | 405 | 37% helix, 20% strand | P40051 |
| B | Apstatin | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- 01B · (2S,3R)-3-amino-2-hydroxy-4-phenylbutanoic acid · ligand · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- NH2 · Amino group · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.50 | 0.83 | 20 | empty |
| 2 | 108 | 0.45 | 0.79 | 16 | empty |
| 3 | 113 | 0.41 | 0.76 | 21 | empty |
| 4 | 107 | 0.41 | 0.77 | 18 | 01B, MN |
| 5 | 57 | 0.37 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 253 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6A9U · Crystal strcture of Icp55 from Saccharomyces cerevisiae bound to apstatin inhibitor · 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 0.97
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 6A9U · PDBe 6A9U · UniProt P40051
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