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Crystal structure of gbs GAPDH
Analyse Crystal structure of gbs GAPDH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y37
- Type
- protein
- Length
- 1,350 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
- Q8E3E8
- Ligands
- NAD, SO4
- Pockets
- 15 · best druggability 0.81
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 | 336 | 27% helix, 29% strand | Q8E3E8 |
| B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 339 | 27% helix, 28% strand | Q8E3E8 |
| C | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 335 | 27% helix, 28% strand | Q8E3E8 |
| D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 340 | 27% helix, 28% strand | Q8E3E8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, D, B, C
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.81 | 0.83 | 111 | empty |
| 2 | 1164 | 0.76 | 0.79 | 105 | NAD, SO4 |
| 3 | 620 | 0.75 | 0.82 | 66 | NAD, SO4 |
| 4 | 308 | 0.63 | 0.80 | 53 | SO4 |
| 5 | 109 | 0.41 | 0.76 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1981 Ų buried · 53 hydrogen bonds · protein-protein
- B–D · 1978 Ų buried · 55 hydrogen bonds · protein-protein
- A–D · 1405 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1363 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 587 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5Y37 · Crystal structure of GBS GAPDH · 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 Q8E3E8
- Elsewhere: RCSB PDB 5Y37 · PDBe 5Y37 · UniProt Q8E3E8
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