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
- 5JYA
- Type
- protein
- Length
- 1,338 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
- Ligands
- NAD, G3H
- Pockets
- 12 · best druggability 0.81
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 | 330 | 26% helix, 28% strand | Q9ALW2 |
| B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 332 | 26% helix, 29% strand | Q9ALW2 |
| C | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 333 | 27% helix, 29% strand | Q9ALW2 |
| D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 343 | 25% helix, 28% strand | Q9ALW2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, C, B, D
- G3H · Glyceraldehyde-3-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.81 | 0.82 | 112 | empty |
| 2 | 1133 | 0.80 | 0.82 | 113 | NAD, G3H |
| 3 | 1130 | 0.80 | 0.82 | 109 | NAD, G3H |
| 4 | 112 | 0.42 | 0.77 | 25 | empty |
| 5 | 110 | 0.40 | 0.76 | 24 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2049 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2026 Ų buried · 48 hydrogen bonds · protein-protein
- B–D · 1457 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1433 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 579 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5JYA · 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 5JYA · PDBe 5JYA · UniProt Q9ALW2
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