MolNFT v1 · #123888 · protein
Structures of streptococcus agalactiae gbs GAPDH in different enzymatic states
5JYE · Glyceraldehyde-3-phosphate dehydrogenase: “Structures of streptococcus agalactiae gbs GAPDH in different enzymatic states”. X-ray diffraction, 2 ligands (NAD, MG), 14 pockets (best druggability 0.82). MolNFT v1 #123888 on GenesisL1…
- PDB
- 5JYE
- Type
- protein
- Length
- 1,339 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
- 14 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, 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 | 337 | 27% helix, 28% strand | Q9ALW2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.82 | 0.83 | 103 | empty |
| 2 | 1012 | 0.79 | 0.81 | 109 | NAD |
| 3 | 645 | 0.65 | 0.75 | 66 | empty |
| 4 | 563 | 0.63 | 0.75 | 59 | empty |
| 5 | 94 | 0.40 | 0.77 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2024 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 2016 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 1388 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1350 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 605 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5JYE · 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 5JYE · PDBe 5JYE · UniProt Q9ALW2
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