MolNFT v1 · #30654 · protein
Crystal structures of SARS coronavirus main peptidase inhibited by an aza-peptide epoxide in space group P212121
2A5K · 3C-like peptidase: “Crystal structures of SARS coronavirus main peptidase inhibited by an aza-peptide epoxide in space group…”. X-ray diffraction, 1 ligand (AZP), 6 pockets (best druggability 0.77). MolNFT v1 #30654 on GenesisL1: 3D…
- PDB
- 2A5K
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- 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
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like peptidase (EC 3.4.22.-) | protein | 304 | 25% helix, 29% strand | P59641 |
| B | 3C-like peptidase (EC 3.4.22.-) | protein | 300 | 26% helix, 29% 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 · 2 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.77 | 0.79 | 76 | empty |
| 2 | 346 | 0.55 | 0.74 | 53 | empty |
| 3 | 217 | 0.54 | 0.78 | 31 | AZP |
| 4 | 239 | 0.54 | 0.77 | 32 | AZP |
| 5 | 182 | 0.48 | 0.76 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1277 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2A5K · Crystal structures of SARS coronavirus main peptidase inhibited by an aza-peptide epoxide… · the same entry in another collection · chain B against B, 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 2A5K · PDBe 2A5K · UniProt P59641
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