MolNFT v1 · #46328 · protein
Crystal structure of a thiamine biosynthesis lipoprotein apbe, northeast strcutural genomics target ER559
2O18: “Crystal structure of a thiamine biosynthesis lipoprotein apbe, northeast strcutural genomics target ER559”. X-ray diffraction, 1 ligand (CA), 17 pockets (best druggability 0.84). MolNFT v1 #46328 on GenesisL1: 3D structure, binding…
- PDB
- 2O18
- Type
- protein
- Length
- 1,226 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiamine biosynthesis lipoprotein apbe
- UniProt
- P0AB85
- Ligands
- CA
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiamine biosynthesis lipoprotein apbe | protein | 307 | 35% helix, 25% strand | P0AB85 |
| B | Thiamine biosynthesis lipoprotein apbe | protein | 300 | 35% helix, 24% strand | P0AB85 |
| C | Thiamine biosynthesis lipoprotein apbe | protein | 313 | 33% helix, 24% strand | P0AB85 |
| D | Thiamine biosynthesis lipoprotein apbe | protein | 306 | 34% helix, 25% strand | P0AB85 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1169 | 0.84 | 0.85 | 84 | empty |
| 2 | 1085 | 0.83 | 0.84 | 81 | empty |
| 3 | 874 | 0.71 | 0.76 | 96 | empty |
| 4 | 611 | 0.70 | 0.78 | 47 | empty |
| 5 | 603 | 0.69 | 0.78 | 55 | CA |
Interfaces
5 interfaces between chains.
- B–D · 1641 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1569 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 370 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 184 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 135 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 2O18 · Crystal structure of a Thiamine biosynthesis lipoprotein apbE, NorthEast Strcutural… · the same entry in another collection · chain D against D, TM-score 1.00
- P0AB85 · AlphaFold monomer V2.0 prediction for FAD:PROTEIN FMN transferase (P0AB85) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P0AB85
- Elsewhere: RCSB PDB 2O18 · PDBe 2O18 · UniProt P0AB85
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