MolNFT v1 · #28225 · protein
1.9 a crystal structure of a protein of unknown function AF1403 from archaeoglobus fulgidus, probable metabolic regulator
1Y7P · Hypothetical protein AF1403: “1.9 a crystal structure of a protein of unknown function AF1403 from archaeoglobus fulgidus, probable…”. X-ray diffraction, 2 ligands (RIP, ZN), 5 pockets (best druggability 0.70). MolNFT v1 #28225 on…
- PDB
- 1Y7P
- Type
- protein
- Length
- 635 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein AF1403
- UniProt
- O28869
- Ligands
- RIP, ZN
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein AF1403 | protein | 212 | 40% helix, 29% strand | O28869 |
| B | Hypothetical protein AF1403 | protein | 217 | 40% helix, 29% strand | O28869 |
| C | Hypothetical protein AF1403 | protein | 206 | 40% helix, 24% strand | O28869 |
Ligands and binding sites
- RIP · beta-D-ribopyranose · ligand · 3 copies · chains A, C, B
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.70 | 0.97 | 16 | empty |
| 2 | 218 | 0.69 | 0.86 | 36 | empty |
| 3 | 287 | 0.66 | 0.82 | 38 | empty |
| 4 | 62 | 0.54 | 0.87 | 17 | empty |
| 5 | 58 | 0.37 | 0.78 | 11 | empty |
Interfaces
1 interface between chains.
- A–C · 2943 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 1Y7P · 1.9 A Crystal Structure of a Protein of Unknown Function AF1403 from Archaeoglobus… · the same entry in another collection · chain A against A, TM-score 1.00
- O28869 · AlphaFold monomer V2.0 prediction for uncharacterized protein AF_1403 (O28869) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O28869
- Elsewhere: RCSB PDB 1Y7P · PDBe 1Y7P · UniProt O28869
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