Research workbench
Crystal structure of unknown funciton protein from synechococcus sp. wh 8102
Analyse Crystal structure of unknown funciton protein from synechococcus sp. wh 8102 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DCI
- Type
- protein
- Length
- 1,168 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q7U8F0
- Ligands
- SO4
- Pockets
- 19 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 53% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Uncharacterized protein | protein | 147 | 54% helix, 24% strand | Q7U8F0 |
| B, C | Uncharacterized protein | protein | 148 | 52% helix, 25% strand | Q7U8F0 |
| D | Uncharacterized protein | protein | 145 | 54% helix, 26% strand | Q7U8F0 |
| G | Uncharacterized protein | protein | 143 | 55% helix, 27% strand | Q7U8F0 |
| H | Uncharacterized protein | protein | 143 | 52% helix, 26% strand | Q7U8F0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D, E, F, G, H
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 | 55 | 0.65 | 0.95 | 16 | empty |
| 2 | 365 | 0.61 | 0.78 | 32 | empty |
| 3 | 99 | 0.61 | 0.88 | 21 | empty |
| 4 | 151 | 0.53 | 0.80 | 25 | empty |
| 5 | 153 | 0.50 | 0.79 | 30 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1348 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 1204 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1128 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1033 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 948 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 4DCI · Crystal structure of unknown funciton protein from Synechococcus sp. WH 8102 · 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 Q7U8F0
- Elsewhere: RCSB PDB 4DCI · PDBe 4DCI · UniProt Q7U8F0
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