Research workbench
Crystal structure of peptiligase mutant - L217H/M222P/A225N/F189W
Analyse Crystal structure of peptiligase mutant - L217H/M222P/A225N/F189W in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AM6
- Type
- protein
- Length
- 810 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Subtilisin bpn'; Leu-pro-glu-gly-ser-pro-val-thr-asp-leu-arg-tyr
- EC
- 3.4.21.62
- UniProt
- P00782
- Pockets
- 6 · best druggability 0.78
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 | 31% helix, 20% strand | P00782 |
| B | Subtilisin bpn' (EC 3.4.21.62) | protein | 269 | 30% helix, 20% strand | P00782 |
| C | Subtilisin bpn' (EC 3.4.21.62) | protein | 267 | 31% helix, 19% strand | P00782 |
| P | Leu-pro-glu-gly-ser-pro-val-thr-asp-leu-arg-tyr | protein | 7 | 0% helix, 29% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 8 copies · chains A, B, C
- TAR · D(-)-tartaric acid · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.78 | 0.82 | 102 | empty |
| 2 | 203 | 0.48 | 0.75 | 37 | empty |
| 3 | 94 | 0.44 | 0.79 | 25 | empty |
| 4 | 81 | 0.42 | 0.80 | 17 | TAR |
| 5 | 58 | 0.35 | 0.78 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–C · 979 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 670 Ų buried · 3 hydrogen bonds · protein-protein
- C–P · 559 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 252 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 modified, 1 covalent (disulfide, oxidation, additive adduct).
Compared structures
- 7AM6 · Crystal structure of Peptiligase mutant - L217H/M222P/A225N/F189W · 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 7AM6 · PDBe 7AM6 · UniProt P00782
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