MolNFT v1 · #40289 · protein
Crystal structure of a hypothetical protein from archaeoglobus fulgidus binding riboflavin 5'-phosphate
2IML: “Crystal structure of a hypothetical protein from archaeoglobus fulgidus binding riboflavin 5'-phosphate”. X-ray diffraction, 1 ligand (FMN), 11 pockets (best druggability 0.81). MolNFT v1 #40289 on GenesisL1: 3D structure, binding…
- PDB
- 2IML
- Type
- protein
- Length
- 768 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- O28442
- Ligands
- FMN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein | protein | 191 | 40% helix, 32% strand | O28442 |
| B, C | Hypothetical protein | protein | 190 | 39% helix, 32% strand | O28442 |
| D | Hypothetical protein | protein | 197 | 39% helix, 31% strand | O28442 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, D
- GOL · Glycerol · additive · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.81 | 0.95 | 22 | GOL |
| 2 | 178 | 0.79 | 0.94 | 22 | GOL |
| 3 | 1152 | 0.74 | 0.77 | 74 | empty |
| 4 | 414 | 0.62 | 0.77 | 40 | FMN |
| 5 | 403 | 0.61 | 0.77 | 38 | FMN |
Interfaces
3 interfaces between chains.
- B–D · 1635 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1628 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 593 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2IML · Crystal structure of a hypothetical protein from Archaeoglobus fulgidus binding… · 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 O28442
- Elsewhere: RCSB PDB 2IML · PDBe 2IML · UniProt O28442
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