Research workbench
Complex between S. aureus aureolysin and wt impi.
Analyse Complex between S. aureus aureolysin and wt impi. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SKM
- Type
- protein
- Length
- 734 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc metalloproteinase aureolysin; Impi alpha
- EC
- 3.4.24.29
- UniProt
- P81177, P82176
- Ligands
- CA, ZN
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc metalloproteinase aureolysin (EC 3.4.24.29) | protein | 301 | 44% helix, 19% strand | P81177 |
| B, D | Impi alpha | protein | 37 | 8% helix, 22% strand | P82176 |
| E | Impi alpha | protein | 30 | 10% helix, 40% strand | P82176 |
| C | Zinc metalloproteinase aureolysin (EC 3.4.24.29) | protein | 300 | 44% helix, 19% strand | P81177 |
| F | Impi alpha | protein | 29 | 10% helix, 41% strand | P82176 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains A, B, C, D, F
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, E
- PEG · Di(hydroxyethyl)ether · additive · 2 copies
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 | 773 | 0.76 | 0.81 | 54 | EDO |
| 2 | 218 | 0.55 | 0.78 | 36 | empty |
| 3 | 176 | 0.50 | 0.78 | 37 | empty |
| 4 | 145 | 0.45 | 0.76 | 23 | empty |
| 5 | 171 | 0.43 | 0.74 | 24 | empty |
Interfaces
10 interfaces between chains.
- B–E · 1038 Ų buried · 32 hydrogen bonds · protein-protein
- D–F · 1004 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 628 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 595 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 416 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7SKM · Complex between S. aureus aureolysin and wt IMPI. · the same entry in another collection · chain F against F, TM-score 1.00
- P81177 · AlphaFold monomer V2.0 prediction for zinc metalloproteinase aureolysin (P81177) · a predicted model of the same protein · chain C against A, TM-score 1.00
- P82176 · AlphaFold monomer V2.0 prediction for inducible metalloproteinase inhibitor protein… · a predicted model of the same protein · chain E against A, TM-score 0.91
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 P81177
- Every structure of UniProt P82176
- Elsewhere: RCSB PDB 7SKM · PDBe 7SKM · UniProt P81177 · UniProt P82176
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