Research workbench
Crystal structure of group a streptococcal surface dehydrogenase (sdh)
Analyse Crystal structure of group a streptococcal surface dehydrogenase (sdh) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ITE
- Type
- protein
- Length
- 1,352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.12
- UniProt
- P0C0G6
- Ligands
- NAD, SO4
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 339 | 28% helix, 28% strand | P0C0G6 |
| Q, R | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 336 | 28% helix, 28% strand | P0C0G6 |
| O | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 341 | 28% helix, 28% strand | P0C0G6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains P, Q, R, O
- SO4 · Sulfate ion · ion · 6 copies · chains P, Q, R, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.81 | 0.84 | 103 | NAD, SO4 |
| 2 | 914 | 0.81 | 0.83 | 89 | empty |
| 3 | 1114 | 0.80 | 0.81 | 120 | NAD, SO4 |
| 4 | 88 | 0.41 | 0.78 | 16 | empty |
| 5 | 105 | 0.38 | 0.75 | 16 | empty |
Interfaces
6 interfaces between chains.
- Q–R · 1996 Ų buried · 37 hydrogen bonds · protein-protein
- P–O · 1990 Ų buried · 34 hydrogen bonds · protein-protein
- R–O · 1467 Ų buried · 16 hydrogen bonds · protein-protein
- P–Q · 1393 Ų buried · 14 hydrogen bonds · protein-protein
- P–R · 476 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6ITE · Crystal structure of group A Streptococcal surface dehydrogenase (SDH) · the same entry in another collection · chain O against O, TM-score 1.00
- P0C0G6 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P0C0G6) · a predicted model of the same protein · chain R 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 P0C0G6
- Elsewhere: RCSB PDB 6ITE · PDBe 6ITE · UniProt P0C0G6
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