MolNFT v1 · #78906 · protein
Crystal structure of SARS coronavirus main protease complexed with ac- estlq-H (cocrystallization)
3SND · 3C-like proteinase: “Crystal structure of SARS coronavirus main protease complexed with ac- estlq-H (cocrystallization)”. X-ray diffraction, 6 pockets (best druggability 0.76). MolNFT v1 #78906 on GenesisL1: 3D structure, binding…
- PDB
- 3SND
- Type
- protein
- Length
- 616 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; Peptide aldehyde inhibitor ac-estlq-H
- EC
- 3.4.22.-
- UniProt
- P0C6U8
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.-) | protein | 306 | 25% helix, 29% strand | P0C6U8 |
| C, D | Peptide aldehyde inhibitor ac-estlq-H | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.76 | 0.78 | 76 | empty |
| 2 | 59 | 0.71 | 0.98 | 21 | empty |
| 3 | 429 | 0.59 | 0.75 | 56 | empty |
| 4 | 155 | 0.48 | 0.77 | 28 | empty |
| 5 | 128 | 0.40 | 0.74 | 27 | MRD |
Interfaces
5 interfaces between chains.
- A–B · 1415 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 323 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 321 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 16 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 3SND · Crystal structure of SARS coronavirus main protease complexed with Ac-ESTLQ-H… · 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 P0C6U8
- Elsewhere: RCSB PDB 3SND · PDBe 3SND · UniProt P0C6U8
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