Research workbench
Crystal structure of C150S mutant glyceraldehyde-3-phosphate DEHYDROGENASE1 from escherichia COLI complexed with bpg at 2.31 ångström resolution
Analyse Crystal structure of C150S mutant glyceraldehyde-3-phosphate DEHYDROGENASE1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C5R
- Type
- protein
- Length
- 1,333 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
- A0A140NCK4
- Ligands
- NAD, G3H, DG4, CL, PO4
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 334 | 30% helix, 28% strand | A0A140NCK4 |
| P, Q, R | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 333 | 30% helix, 28% strand | A0A140NCK4 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains O, R, P, Q
- G3H · Glyceraldehyde-3-phosphate · ligand · 3 copies · chains P, Q, R
- DG4 · phosphono (2S)-2-oxidanyl-3-phosphonooxy-propanoate · ligand · chains O
- CL · Chloride ion · ion · 8 copies · chains O, P, Q, R
- PO4 · Phosphate ion · ion · 5 copies · chains O, P, Q, R
- EDO · 1,2-ethanediol · additive · 5 copies · chains O, P, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.77 | 0.79 | 114 | NAD, DG4, CL, G3H |
| 2 | 699 | 0.73 | 0.79 | 88 | PO4 |
| 3 | 619 | 0.72 | 0.80 | 63 | NAD, G3H |
| 4 | 467 | 0.69 | 0.80 | 58 | NAD, G3H, CL |
| 5 | 302 | 0.56 | 0.76 | 32 | empty |
Interfaces
6 interfaces between chains.
- O–P · 2014 Ų buried · 46 hydrogen bonds · protein-protein
- Q–R · 2012 Ų buried · 46 hydrogen bonds · protein-protein
- O–R · 1425 Ų buried · 20 hydrogen bonds · protein-protein
- P–Q · 1420 Ų buried · 20 hydrogen bonds · protein-protein
- O–Q · 580 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7C5R · Crystal Structure of C150S mutant Glyceraldehyde-3-phosphate dehydrogenase1 from… · the same entry in another collection · chain O against O, 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 A0A140NCK4
- Elsewhere: RCSB PDB 7C5R · PDBe 7C5R · UniProt A0A140NCK4
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