Research workbench
Structures of streptococcus agalactiae gbs GAPDH in different enzymatic states
Analyse Structures of streptococcus agalactiae gbs GAPDH in different enzymatic states in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JYF
- Type
- protein
- Length
- 1,272 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.-
- UniProt
- Q9ALW2
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 324 | 26% helix, 30% strand | Q9ALW2 |
| B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 294 | 27% helix, 25% strand | Q9ALW2 |
| C | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 334 | 28% helix, 28% strand | Q9ALW2 |
| D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 320 | 25% helix, 28% strand | Q9ALW2 |
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.85 | 0.86 | 99 | empty |
| 2 | 792 | 0.72 | 0.78 | 99 | empty |
| 3 | 963 | 0.70 | 0.75 | 114 | empty |
| 4 | 341 | 0.63 | 0.79 | 40 | empty |
| 5 | 62 | 0.52 | 0.86 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2028 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2025 Ų buried · 51 hydrogen bonds · protein-protein
- B–D · 1352 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1290 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 615 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5JYF · Structures of Streptococcus agalactiae GBS GAPDH in different enzymatic states · 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 Q9ALW2
- Elsewhere: RCSB PDB 5JYF · PDBe 5JYF · UniProt Q9ALW2
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