Research workbench
Crystal structure of peptiligase mutant - M222P/L217H/A225N/F189W/N218D
Analyse Crystal structure of peptiligase mutant - M222P/L217H/A225N/F189W/N218D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AM7
- Type
- protein
- Length
- 806 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Subtilisin bpn'; Eglin C fragment
- EC
- 3.4.21.62
- UniProt
- P00782
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Subtilisin bpn' (EC 3.4.21.62) | protein | 267 | 30% helix, 19% strand | P00782 |
| B | Subtilisin bpn' (EC 3.4.21.62) | protein | 268 | 31% helix, 20% strand | P00782 |
| C | Subtilisin bpn' (EC 3.4.21.62) | protein | 265 | 31% helix, 19% strand | P00782 |
| P | Eglin C fragment | protein | 6 | 0% helix, 33% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
- GOL · Glycerol · additive · 9 copies · chains A, B, C
- PGE · Triethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.73 | 0.84 | 59 | empty |
| 2 | 393 | 0.70 | 0.82 | 43 | empty |
| 3 | 198 | 0.52 | 0.77 | 36 | empty |
| 4 | 88 | 0.50 | 0.83 | 28 | empty |
| 5 | 63 | 0.38 | 0.79 | 16 | empty |
Interfaces
4 interfaces between chains.
- B–C · 959 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 722 Ų buried · 3 hydrogen bonds · protein-protein
- C–P · 488 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 239 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 modified (disulfide, oxidation).
Compared structures
- 7AM7 · Crystal structure of Peptiligase mutant - M222P/L217H/A225N/F189W/N218D · 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 P00782
- Elsewhere: RCSB PDB 7AM7 · PDBe 7AM7 · UniProt P00782
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