MolNFT v1 · #100024 · protein
Crystal structure of uncharacterized tim barrel protein with the conserved phosphate binding site fromsebaldella termitidis
4ML9 · Uncharacterized protein: “Crystal structure of uncharacterized tim barrel protein with the conserved phosphate binding site…”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability 0.65). MolNFT v1 #100024 on GenesisL1: 3D…
- 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
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