MolNFT v1 · #78116 · protein
Crystal structure of a tripeptidase (SAV1512) from staphylococcus aureus subsp. aureus MU50 at 2.10 a resolution
3RZA: “Crystal structure of a tripeptidase (SAV1512) from staphylococcus aureus subsp. aureus MU50 at 2.10 a…”. X-ray diffraction, 2 ligands (CA, ZN), 4 pockets (best druggability 0.62). MolNFT v1 #78116 on GenesisL1: 3D structure, binding…
- PDB
- 3RZA
- Type
- protein
- Length
- 746 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tripeptidase
- UniProt
- Q99TY1
- Ligands
- CA, ZN
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tripeptidase | protein | 373 | 35% helix, 27% strand | Q99TY1 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
- IPA · Isopropyl alcohol · additive · chains A, B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.62 | 0.78 | 41 | CIT |
| 2 | 376 | 0.61 | 0.78 | 39 | CIT |
| 3 | 99 | 0.43 | 0.78 | 19 | empty |
| 4 | 95 | 0.39 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1438 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3RZA · Crystal structure of a tripeptidase (SAV1512) from staphylococcus aureus subsp. aureus… · 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 Q99TY1
- Elsewhere: RCSB PDB 3RZA · PDBe 3RZA · UniProt Q99TY1
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