Research workbench
X-ray structure of pedv papain-like protease 2 bound to ub-pa
Analyse X-ray structure of pedv papain-like protease 2 bound to ub-pa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MC9
- Type
- protein
- Length
- 2,465 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; Ubiquitin
- EC
- 3.4.19.12, 3.6.4.12, 3.6.4.13
- UniProt
- A0A0S3MQV7, P0CG47
- Ligands
- AYE, ZN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 27% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 3C-like proteinase (EC 3.4.19.12, 3.6.4.12, 3.6.4.13) | protein | 233 | 28% helix, 36% strand | A0A0S3MQV7 |
| B, D, F, H, J, L, N, P | Ubiquitin | protein | 75 | 20% helix, 33% strand | P0CG47 |
| E | 3C-like proteinase (EC 3.4.19.12, 3.6.4.12, 3.6.4.13) | protein | 230 | 28% helix, 30% strand | A0A0S3MQV7 |
| G | 3C-like proteinase (EC 3.4.19.12, 3.6.4.12, 3.6.4.13) | protein | 232 | 28% helix, 34% strand | A0A0S3MQV7 |
| I, K, O | 3C-like proteinase (EC 3.4.19.12, 3.6.4.12, 3.6.4.13) | protein | 235 | 27% helix, 33% strand | A0A0S3MQV7 |
| M | 3C-like proteinase (EC 3.4.19.12, 3.6.4.12, 3.6.4.13) | protein | 232 | 25% helix, 34% strand | A0A0S3MQV7 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · 8 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- ZN · Zinc ion · metal · 14 copies · chains A, O, C, E, K, G, I, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.84 | 0.85 | 116 | empty |
| 2 | 1123 | 0.82 | 0.84 | 125 | empty |
| 3 | 1055 | 0.82 | 0.83 | 122 | empty |
| 4 | 951 | 0.82 | 0.84 | 130 | empty |
| 5 | 910 | 0.81 | 0.83 | 116 | empty |
Interfaces
38 interfaces between chains.
- M–N · 978 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 972 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 969 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 961 Ų buried · 15 hydrogen bonds · protein-protein
- O–P · 949 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 7MC9 · X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA · the same entry in another collection · chain C against C, 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 A0A0S3MQV7
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 7MC9 · PDBe 7MC9 · UniProt A0A0S3MQV7 · UniProt P0CG47
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