Research workbench
Streptococcus pneumoniae glyceraldehyde-3-phosphate dehydrogenase (spgapdh) crystal structure
Analyse Streptococcus pneumoniae glyceraldehyde-3-phosphate dehydrogenase (spgapdh)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M6D
- Type
- protein
- Length
- 680 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.-
- UniProt
- I6L8L9
- Ligands
- CA, CL
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 346 | 28% helix, 28% strand | I6L8L9 |
| B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 334 | 27% helix, 29% strand | I6L8L9 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains B
- ACY · Acetic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.60 | 0.75 | 57 | GOL |
| 2 | 257 | 0.51 | 0.75 | 35 | empty |
| 3 | 84 | 0.36 | 0.76 | 19 | empty |
| 4 | 65 | 0.35 | 0.77 | 22 | ACY |
| 5 | 67 | 0.33 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2027 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5M6D · Streptococcus pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (SpGAPDH) crystal… · 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 I6L8L9
- Elsewhere: RCSB PDB 5M6D · PDBe 5M6D · UniProt I6L8L9
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