Research workbench
Structure of the S. aureus amidase lyth and activator acth extracellular domains
Analyse Structure of the S. aureus amidase lyth and activator acth extracellular domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TJ4
- Type
- protein
- Length
- 595 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acth; Lyth
- EC
- 3.4.21.105, 3.5.1.-
- UniProt
- A0A2X3YEX3, O32421
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Acth (EC 3.4.21.105) | protein | 122 | 75% helix, 0% strand | A0A2X3YEX3 |
| B | Lyth (EC 3.5.1.-) | protein | 176 | 38% helix, 21% strand | O32421 |
| D | Lyth (EC 3.5.1.-) | protein | 175 | 38% helix, 23% strand | O32421 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, D
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 | 220 | 0.64 | 0.83 | 48 | empty |
| 2 | 108 | 0.46 | 0.79 | 25 | empty |
| 3 | 169 | 0.44 | 0.75 | 25 | empty |
| 4 | 95 | 0.44 | 0.79 | 18 | empty |
| 5 | 139 | 0.43 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1080 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1069 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 750 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7TJ4 · Structure of the S. aureus amidase LytH and activator ActH extracellular domains · the same entry in another collection · chain A against A, TM-score 1.00
- O32421 · AlphaFold monomer V2.0 prediction for probable cell wall amidase lyth (O32421) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 A0A2X3YEX3
- Every structure of UniProt O32421
- Elsewhere: RCSB PDB 7TJ4 · PDBe 7TJ4 · UniProt A0A2X3YEX3 · UniProt O32421
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