MolNFT v1 · #119964 · protein
Crystal structure of TON_0340 in complex with mg
5GL3 · Uncharacterized protein: “Crystal structure of TON_0340 in complex with mg”. X-ray diffraction, 1 ligand (MG), 16 pockets (best druggability 0.86). MolNFT v1 #119964 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GL3
- Type
- protein
- Length
- 1,604 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- B6YTD8
- Ligands
- MG
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | Uncharacterized protein | protein | 269 | 45% helix, 16% strand | B6YTD8 |
| B | Uncharacterized protein | protein | 260 | 44% helix, 17% strand | B6YTD8 |
| C | Uncharacterized protein | protein | 268 | 45% helix, 15% strand | B6YTD8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.86 | 0.87 | 117 | empty |
| 2 | 985 | 0.79 | 0.81 | 101 | empty |
| 3 | 106 | 0.75 | 0.95 | 21 | empty |
| 4 | 357 | 0.62 | 0.78 | 46 | MG |
| 5 | 231 | 0.62 | 0.81 | 26 | MG |
Interfaces
9 interfaces between chains.
- C–F · 1366 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1247 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 931 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 601 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 584 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5GL3 · Crystal structure of TON_0340 in complex with Mg · 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 B6YTD8
- Elsewhere: RCSB PDB 5GL3 · PDBe 5GL3 · UniProt B6YTD8
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