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Crystal structure of an uncharacterized protein (O28723_ARCFU) from archaeoglobus fulgidus
Analyse Crystal structure of an uncharacterized protein (O28723_ARCFU) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BPD
- Type
- protein
- Length
- 1,273 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- O28723
- Ligands
- MG
- Pockets
- 19 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, K | Uncharacterized protein | protein | 91 | 20% helix, 51% strand | O28723 |
| B, C, E, G, H, J, L, M | Uncharacterized protein | protein | 91 | 21% helix, 47% strand | O28723 |
| F | Uncharacterized protein | protein | 92 | 21% helix, 50% strand | O28723 |
| I, N | Uncharacterized protein | protein | 90 | 20% helix, 48% strand | O28723 |
Ligands and binding sites
- MG · Magnesium ion · metal · 27 copies · chains A, H, B, I, C, J, D, K, E, L, F, M, G, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.58 | 0.86 | 21 | empty |
| 2 | 60 | 0.52 | 0.87 | 15 | empty |
| 3 | 52 | 0.51 | 0.88 | 19 | empty |
| 4 | 60 | 0.50 | 0.86 | 18 | empty |
| 5 | 71 | 0.48 | 0.83 | 20 | empty |
Interfaces
28 interfaces between chains.
- A–G · 851 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 838 Ų buried · 11 hydrogen bonds · protein-protein
- J–K · 829 Ų buried · 12 hydrogen bonds · protein-protein
- H–I · 829 Ų buried · 11 hydrogen bonds · protein-protein
- H–N · 826 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 3BPD · Crystal structure of an uncharacterized protein (O28723_ARCFU) from Archaeoglobus fulgidus · 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 O28723
- Elsewhere: RCSB PDB 3BPD · PDBe 3BPD · UniProt O28723
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