Research workbench
Co-enzyme induced conformational changes in bovine eye glyceraldehyde 3-phosphate dehydrogenase
Analyse Co-enzyme induced conformational changes in bovine eye glyceraldehyde… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O59
- Type
- protein
- Length
- 1,328 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, 2.6.99.-
- UniProt
- P10096
- Ligands
- NAD
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, P, R, Q | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12, 2.6.99.-) | protein | 332 | 32% helix, 27% strand | P10096 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains O, R, P, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.83 | 0.85 | 107 | empty |
| 2 | 620 | 0.72 | 0.79 | 77 | NAD |
| 3 | 521 | 0.69 | 0.79 | 60 | NAD |
| 4 | 500 | 0.69 | 0.79 | 57 | NAD |
| 5 | 499 | 0.69 | 0.79 | 61 | NAD |
Interfaces
6 interfaces between chains.
- O–P · 2027 Ų buried · 29 hydrogen bonds · protein-protein
- R–Q · 2024 Ų buried · 31 hydrogen bonds · protein-protein
- O–R · 1366 Ų buried · 25 hydrogen bonds · protein-protein
- P–Q · 1361 Ų buried · 22 hydrogen bonds · protein-protein
- P–R · 542 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4O59 · Co-enzyme Induced Conformational Changes in Bovine Eye Glyceraldehyde 3-Phosphate… · the same entry in another collection · chain Q against Q, TM-score 1.00
- P10096 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P10096) · a predicted model of the same protein · chain R 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 P10096
- Elsewhere: RCSB PDB 4O59 · PDBe 4O59 · UniProt P10096
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