Research workbench
The crystal structure of xmrv protease complexed with pepstatin a
Analyse The crystal structure of xmrv protease complexed with pepstatin a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SM1
- Type
- protein
- Length
- 231 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag-pro-pol polyprotein; Pepstatin a
- UniProt
- Q9E7M1
- Ligands
- IVA
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gag-pro-pol polyprotein | protein | 113 | 6% helix, 50% strand | Q9E7M1 |
| B | Gag-pro-pol polyprotein | protein | 112 | 6% helix, 50% strand | Q9E7M1 |
| J, M | Pepstatin a | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- IVA · Isovaleric acid · ligand · 2 copies · chains A, B, J, M
- FMT · Formic acid · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.73 | 0.96 | 28 | IVA |
Interfaces
5 interfaces between chains.
- A–B · 1325 Ų buried · 18 hydrogen bonds · protein-protein
- B–J · 351 Ų buried · 7 hydrogen bonds · protein-protein
- A–M · 332 Ų buried · 5 hydrogen bonds · protein-protein
- A–J · 80 Ų buried · 0 hydrogen bonds · protein-protein
- B–M · 71 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 3SM1 · The crystal structure of XMRV protease complexed with pepstatin A · 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 Q9E7M1
- Elsewhere: RCSB PDB 3SM1 · PDBe 3SM1 · UniProt Q9E7M1
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