Research workbench
X-ray structure of mhv PLP2 (CYS1716SER) catalytic mutant in complex with free ubiquitin
Analyse X-ray structure of mhv PLP2 (CYS1716SER) catalytic mutant in complex with free… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WFI
- Type
- protein
- Length
- 756 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Papain-like protease; Ubiquitin
- EC
- 3.4.22.-
- UniProt
- P0C6X9, P0CG47
- Ligands
- ZN
- Pockets
- 13 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Papain-like protease (EC 3.4.22.-) | protein | 301 | 28% helix, 36% strand | P0C6X9 |
| B | Papain-like protease (EC 3.4.22.-) | protein | 303 | 28% helix, 36% strand | P0C6X9 |
| C, D | Ubiquitin | protein | 76 | 24% helix, 34% strand | P0CG47 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B, C, D
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.59 | 0.80 | 25 | empty |
| 2 | 281 | 0.59 | 0.78 | 29 | GOL |
| 3 | 288 | 0.58 | 0.78 | 35 | GOL |
| 4 | 129 | 0.53 | 0.81 | 23 | empty |
| 5 | 105 | 0.45 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1150 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1111 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 353 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5WFI · X-ray structure of MHV PLP2 (Cys1716Ser) catalytic mutant in complex with free ubiquitin · 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 P0C6X9
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5WFI · PDBe 5WFI · UniProt P0C6X9 · UniProt P0CG47
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