Research workbench
Crystal structure of uncharacterized tim barrel protein with the conserved phosphate binding site fromsebaldella termitidis
Analyse Crystal structure of uncharacterized tim barrel protein with the conserved… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ML9
- Type
- protein
- Length
- 551 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- D1AMR0
- Ligands
- MG
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 276 | 52% helix, 14% strand | D1AMR0 |
| B | Uncharacterized protein | protein | 275 | 50% helix, 14% strand | D1AMR0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.65 | 0.79 | 41 | EDO, GOL |
| 2 | 309 | 0.59 | 0.78 | 38 | EDO, GOL |
| 3 | 76 | 0.35 | 0.76 | 16 | empty |
| 4 | 54 | 0.34 | 0.78 | 18 | empty |
| 5 | 71 | 0.33 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2260 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 4ML9 · Crystal Structure of Uncharacterized TIM Barrel Protein with the Conserved Phosphate… · 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 D1AMR0
- Elsewhere: RCSB PDB 4ML9 · PDBe 4ML9 · UniProt D1AMR0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.