Research workbench
Crystal structures of SARS coronavirus main peptidase inhibited by an aza-peptide epoxide in the space group C2
Analyse Crystal structures of SARS coronavirus main peptidase inhibited by an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A5I
- Type
- protein
- Length
- 306 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like peptidase
- EC
- 3.4.22.-
- UniProt
- P59641
- Ligands
- AZP
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like peptidase (EC 3.4.22.-) | protein | 306 | 25% helix, 28% strand | P59641 |
Ligands and binding sites
- AZP · (5S,8S,14R)-ethyl 11-(3-amino-3-oxopropyl)-8-benzyl-14-hydroxy-5-isobutyl-3,6,9,12-tetraoxo-1-phenyl-2-oxa-4,7,10,11-tetraazapentadecan-15-oate · ligand · chains A
- EDO · 1,2-ethanediol · additive · chains A
- GOL · Glycerol · additive · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.48 | 0.76 | 27 | AZP |
| 2 | 115 | 0.39 | 0.75 | 22 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2A5I · Crystal structures of SARS coronavirus main peptidase inhibited by an aza-peptide epoxide… · 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 P59641
- Elsewhere: RCSB PDB 2A5I · PDBe 2A5I · UniProt P59641
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