Research workbench
Glycosylation associate protein (GAP123) complex from streptococcus agalactiae
Analyse Glycosylation associate protein (GAP123) complex 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
- 6OYC
- Type
- protein
- Length
- 1,325 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosylation associate protein 1; Glycosylation associate protein 2; Glycosylation…
- UniProt
- Q8DYM4, Q8DYM5, Q8DYM6
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosylation associate protein 1 | protein | 498 | 34% helix, 24% strand | Q8DYM4 |
| B | Glycosylation associate protein 2 | protein | 517 | 31% helix, 31% strand | Q8DYM5 |
| C | Glycosylation associate protein 3 | protein | 310 | 23% helix, 30% strand | Q8DYM6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 13 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.87 | 0.88 | 93 | empty |
| 2 | 443 | 0.67 | 0.79 | 50 | GOL |
| 3 | 385 | 0.63 | 0.78 | 45 | GOL |
| 4 | 144 | 0.63 | 0.86 | 31 | empty |
| 5 | 195 | 0.59 | 0.81 | 42 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2320 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 1415 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 795 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6OYC · Glycosylation Associate Protein (Gap123) complex 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 Q8DYM4
- Every structure of UniProt Q8DYM5
- Every structure of UniProt Q8DYM6
- Elsewhere: RCSB PDB 6OYC · PDBe 6OYC · UniProt Q8DYM4 · UniProt Q8DYM5 · UniProt Q8DYM6
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