Research workbench
Structure of E.COLI GAPDH rat sperm GAPDH heterotetramer
Analyse Structure of E.COLI GAPDH rat sperm GAPDH heterotetramer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VYV
- Type
- protein
- Length
- 1,324 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
- P0A9B2, Q9ESV6
- Ligands
- NAD, 1GP
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 330 | 31% helix, 28% strand | P0A9B2 |
| D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 334 | 32% helix, 26% strand | Q9ESV6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C
- 1GP · Sn-glycerol-1-phosphate · ligand · chains D
- FMT · Formic acid · additive · 14 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.79 | 0.81 | 126 | FMT |
| 2 | 700 | 0.71 | 0.78 | 68 | NAD |
| 3 | 691 | 0.70 | 0.78 | 68 | NAD |
| 4 | 660 | 0.69 | 0.77 | 80 | FMT, NAD |
| 5 | 588 | 0.68 | 0.77 | 65 | 1GP, FMT, NAD |
Interfaces
6 interfaces between chains.
- B–D · 2048 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 2046 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 1412 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1356 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 618 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (oxidation).
Compared structures
- 2VYV · Structure of E.Coli GAPDH Rat Sperm GAPDH heterotetramer · the same entry in another collection · chain D against D, TM-score 1.00
- P0A9B2 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase a (P0A9B2) · a predicted model of the same protein · chain B against A, TM-score 1.00
- Q9ESV6 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase… · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P0A9B2
- Every structure of UniProt Q9ESV6
- Elsewhere: RCSB PDB 2VYV · PDBe 2VYV · UniProt P0A9B2 · UniProt Q9ESV6
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