Research workbench
Abiei antitoxin from streptococcus agalactiae
Analyse Abiei antitoxin from streptococcus agalactiae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y8Q
- Type
- protein
- Length
- 769 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Abortive phage infection protein
- UniProt
- A0A0E1ENP6
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Abortive phage infection protein | protein | 195 | 46% helix, 17% strand | A0A0E1ENP6 |
| D | Abortive phage infection protein | protein | 184 | 48% helix, 16% strand | A0A0E1ENP6 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B, C
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.68 | 0.79 | 47 | empty |
| 2 | 282 | 0.57 | 0.77 | 31 | B3P |
| 3 | 299 | 0.55 | 0.75 | 32 | empty |
| 4 | 307 | 0.54 | 0.74 | 32 | TRS |
Interfaces
4 interfaces between chains.
- A–C · 536 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 435 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 433 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 119 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6Y8Q · AbiEi antitoxin from Streptococcus agalactiae · 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 A0A0E1ENP6
- Elsewhere: RCSB PDB 6Y8Q · PDBe 6Y8Q · UniProt A0A0E1ENP6
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