MolNFT v1 · #123880 · protein
Structures of streptococcus agalactiae gbs GAPDH in different enzymatic states
5JY6 · Glyceraldehyde-3-phosphate dehydrogenase: “Structures of streptococcus agalactiae gbs GAPDH in different enzymatic states”. X-ray diffraction, 2 ligands (NAD, MG), 13 pockets (best druggability 0.80). MolNFT v1 #123880 on GenesisL1…
- PDB
- 5JY6
- Type
- protein
- Length
- 1,332 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, MG
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 334 | 28% helix, 28% strand | Q9ALW2 |
| B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 335 | 27% helix, 28% strand | Q9ALW2 |
| C | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 330 | 27% helix, 28% strand | Q9ALW2 |
| D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 333 | 28% helix, 28% strand | Q9ALW2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.80 | 0.82 | 112 | empty |
| 2 | 1129 | 0.80 | 0.81 | 109 | NAD |
| 3 | 1134 | 0.79 | 0.81 | 112 | NAD |
| 4 | 103 | 0.39 | 0.76 | 24 | empty |
| 5 | 107 | 0.38 | 0.75 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2013 Ų buried · 52 hydrogen bonds · protein-protein
- C–D · 2002 Ų buried · 50 hydrogen bonds · protein-protein
- B–D · 1401 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1388 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 598 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5JY6 · 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 5JY6 · PDBe 5JY6 · UniProt Q9ALW2
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