MolNFT v1 · #25478 · protein
Crystal structure of holo-glyceraldehyde 3-phosphate dehydrogenase from cryptosporidium parvum
1VSV · Glyceraldehyde-3-phosphate dehydrogenase: “Crystal structure of holo-glyceraldehyde 3-phosphate dehydrogenase from cryptosporidium parvum”. X-ray diffraction, 1 ligand (NAD), 8 pockets (best druggability 0.79). MolNFT v1 #25478 on…
- PDB
- 1VSV
- 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
- NAD
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 26% 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, 26% strand | Q7YYQ9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.79 | 0.81 | 150 | empty |
| 2 | 938 | 0.79 | 0.81 | 111 | NAD |
| 3 | 530 | 0.75 | 0.82 | 58 | NAD |
| 4 | 569 | 0.74 | 0.82 | 61 | NAD |
| 5 | 92 | 0.32 | 0.72 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2001 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1998 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1401 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1341 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 520 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1VSV · Crystal Structure of holo-glyceraldehyde 3-phosphate dehydrogenase from Cryptosporidium… · 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 1VSV · PDBe 1VSV · UniProt Q7YYQ9
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