MolNFT v1 · #59785 · protein
Crystal structure of a possible transciptional regulator yggd from shigella flexneri 2A str. 2457T
3C8G · Putative transcriptional regulator: “Crystal structure of a possible transciptional regulator yggd from shigella flexneri 2A str. 2457T”. X-ray diffraction, 8 pockets (best druggability 0.61). MolNFT v1 #59785 on GenesisL1: 3D…
- PDB
- 3C8G
- Type
- protein
- Length
- 660 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative transcriptional regulator
- UniProt
- Q83Q96
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative transcriptional regulator | protein | 166 | 72% helix, 0% strand | Q83Q96 |
| B | Putative transcriptional regulator | protein | 166 | 71% helix, 0% strand | Q83Q96 |
| C | Putative transcriptional regulator | protein | 167 | 69% helix, 0% strand | Q83Q96 |
| D | Putative transcriptional regulator | protein | 161 | 73% helix, 0% strand | Q83Q96 |
Ligands and binding sites
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.61 | 0.79 | 25 | empty |
| 2 | 280 | 0.55 | 0.76 | 36 | empty |
| 3 | 148 | 0.52 | 0.79 | 29 | empty |
| 4 | 128 | 0.41 | 0.75 | 22 | empty |
| 5 | 66 | 0.37 | 0.78 | 12 | empty |
Interfaces
3 interfaces between chains.
- B–C · 883 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 611 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 528 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (methylation, engineered).
Compared structures
- 3C8G · Crystal structure of a possible transciptional regulator YggD from Shigella flexneri 2a… · the same entry in another collection · chain D against D, TM-score 1.00
- Q83Q96 · AlphaFold monomer V2.0 prediction for fumarase E (Q83Q96) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q83Q96
- Elsewhere: RCSB PDB 3C8G · PDBe 3C8G · UniProt Q83Q96
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