MolNFT v1 · #70042 · protein
Crystal structure of a probable thiamine pyrophosphokinase from staphylococcus saprophyticus subsp. saprophyticus. northeast structural genomics consortium target id SYR86
3L8M: “Crystal structure of a probable thiamine pyrophosphokinase from staphylococcus saprophyticus subsp.…”. X-ray diffraction, 1 ligand (NA), 9 pockets (best druggability 0.68). MolNFT v1 #70042 on GenesisL1: 3D structure, binding sites…
- PDB
- 3L8M
- Type
- protein
- Length
- 370 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable thiamine pyrophosphokinase
- UniProt
- Q49X04
- Ligands
- NA
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable thiamine pyrophosphokinase | protein | 193 | 25% helix, 30% strand | Q49X04 |
| B | Probable thiamine pyrophosphokinase | protein | 177 | 23% helix, 32% strand | Q49X04 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.68 | 0.82 | 39 | empty |
| 2 | 275 | 0.60 | 0.79 | 29 | empty |
| 3 | 312 | 0.58 | 0.77 | 32 | empty |
| 4 | 173 | 0.52 | 0.78 | 35 | empty |
| 5 | 55 | 0.51 | 0.87 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1286 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3L8M · Crystal Structure of a probable thiamine pyrophosphokinase from Staphylococcus… · 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 Q49X04
- Elsewhere: RCSB PDB 3L8M · PDBe 3L8M · UniProt Q49X04
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