Research workbench
Crystal structure of C153S mutant glyceraldehyde 3-phosphate dehydrogenase from cryptosporidium parvum
Analyse Crystal structure of C153S mutant glyceraldehyde 3-phosphate dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CIF
- 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
- Q7YYQ9
- Ligands
- G3H, NAD, MG
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 338 | 30% helix, 27% strand | Q7YYQ9 |
Ligands and binding sites
- G3H · Glyceraldehyde-3-phosphate · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C
- MG · Magnesium ion · metal · 2 copies · chains B, D
- GOL · Glycerol · additive · 2 copies · chains B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.80 | 0.82 | 136 | empty |
| 2 | 597 | 0.76 | 0.82 | 60 | G3H, NAD |
| 3 | 634 | 0.76 | 0.82 | 67 | NAD, GOL, G3H |
| 4 | 540 | 0.73 | 0.81 | 58 | G3H, NAD, MG |
| 5 | 518 | 0.73 | 0.81 | 62 | G3H, NAD |
Interfaces
6 interfaces between chains.
- C–D · 2008 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1997 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1412 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1407 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 538 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3CIF · Crystal Structure of C153S mutant glyceraldehyde 3-phosphate dehydrogenase from… · 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 Q7YYQ9
- Elsewhere: RCSB PDB 3CIF · PDBe 3CIF · UniProt Q7YYQ9
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