MolNFT v1 · #189220 · protein
Crystal structure of sortase a from streptococcus pyogenes in complex with ML346
7V6K: “Crystal structure of sortase a from streptococcus pyogenes in complex with ML346”. X-ray diffraction, 2 ligands (5TI, MG), 3 pockets (best druggability 0.60). MolNFT v1 #189220 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7V6K
- Type
- protein
- Length
- 315 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sortase
- UniProt
- A0A4U7I1I9
- Ligands
- 5TI, MG
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sortase | protein | 158 | 18% helix, 39% strand | A0A4U7I1I9 |
| B | Sortase | protein | 157 | 17% helix, 38% strand | A0A4U7I1I9 |
Ligands and binding sites
- 5TI · 5-[3-(4-methoxyphenyl)prop-2-enylidene]-1,3-diazinane-2,4,6-trione · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.60 | 0.81 | 34 | 5TI |
| 2 | 156 | 0.47 | 0.76 | 27 | 5TI |
| 3 | 65 | 0.31 | 0.74 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 592 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7V6K · Crystal structure of Sortase A from Streptococcus pyogenes in complex with ML346 · 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 A0A4U7I1I9
- Elsewhere: RCSB PDB 7V6K · PDBe 7V6K · UniProt A0A4U7I1I9
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