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Crystal structure of dimeric M-pmv protease D26N mutant in complex with inhibitor
Analyse Crystal structure of dimeric M-pmv protease D26N mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S1V
- Type
- protein
- Length
- 215 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag-pro-pol polyprotein; Pro-0A1-val-psa-ala-met-thr
- EC
- 3.6.1.23, 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-
- UniProt
- P07572
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gag-pro-pol polyprotein (EC 3.6.1.23, 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 103 | 9% helix, 40% strand | P07572 |
| B | Gag-pro-pol polyprotein (EC 3.6.1.23, 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 105 | 9% helix, 41% strand | P07572 |
| I | Pro-0A1-val-psa-ala-met-thr | protein | 7 | 0% helix, 29% strand | — |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.51 | 0.77 | 29 | empty |
| 2 | 56 | 0.32 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1438 Ų buried · 30 hydrogen bonds · protein-protein
- B–I · 453 Ų buried · 5 hydrogen bonds · protein-protein
- A–I · 411 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6S1V · Crystal structure of dimeric M-PMV protease D26N mutant in complex with inhibitor · 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 P07572
- Elsewhere: RCSB PDB 6S1V · PDBe 6S1V · UniProt P07572
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