MolNFT v1 · #119965 · protein
Crystal structure of TON_0340 in complex with mn
5GL4 · Uncharacterized protein: “Crystal structure of TON_0340 in complex with mn”. X-ray diffraction, 1 ligand (MN), 18 pockets (best druggability 0.79). MolNFT v1 #119965 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GL4
- Type
- protein
- Length
- 1,590 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- B6YTD8
- Ligands
- MN
- Pockets
- 18 · best druggability 0.79
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 | 46% helix, 15% strand | B6YTD8 |
| B | Uncharacterized protein | protein | 258 | 45% helix, 17% strand | B6YTD8 |
| C | Uncharacterized protein | protein | 256 | 44% helix, 17% strand | B6YTD8 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 17 copies · chains A, B, C, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.79 | 0.81 | 83 | MN |
| 2 | 844 | 0.79 | 0.82 | 76 | empty |
| 3 | 632 | 0.79 | 0.84 | 65 | empty |
| 4 | 1134 | 0.78 | 0.80 | 110 | empty |
| 5 | 118 | 0.76 | 0.95 | 21 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1266 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 1101 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 891 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 609 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 600 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5GL4 · Crystal structure of TON_0340 in complex with Mn · 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 5GL4 · PDBe 5GL4 · UniProt B6YTD8
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