MolNFT v1 · #125174 · protein
Crystal structure of N-terminus truncated selenophosphate synthetase from leishmania major
5L16 · Putative selenophosphate synthetase: “Crystal structure of N-terminus truncated selenophosphate synthetase from leishmania major”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.53). MolNFT v1 #125174 on…
- PDB
- 5L16
- Type
- protein
- Length
- 323 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative selenophosphate synthetase
- EC
- 2.7.9.3
- UniProt
- Q4Q0M0
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative selenophosphate synthetase (EC 2.7.9.3) | protein | 323 | 37% helix, 28% strand | Q4Q0M0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.53 | 0.86 | 23 | empty |
| 2 | 96 | 0.47 | 0.80 | 21 | empty |
| 3 | 58 | 0.42 | 0.81 | 19 | empty |
| 4 | 107 | 0.39 | 0.76 | 23 | empty |
Compared structures
- 5L16 · Crystal Structure of N-terminus truncated selenophosphate synthetase from Leishmania major · the same entry in another collection · chain A against A, TM-score 1.00
- Q4Q0M0 · AlphaFold monomer V2.0 prediction for selenide, water dikinase (Q4Q0M0) · a predicted model of the same protein · chain A 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 Q4Q0M0
- Elsewhere: RCSB PDB 5L16 · PDBe 5L16 · UniProt Q4Q0M0
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