Research workbench
Crystal structure and functional analysis of glyceraldehyde- 3-phosphate dehydrogenase from oryza sativa
Analyse Crystal structure and functional analysis of glyceraldehyde- 3-phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E6A
- Type
- protein
- Length
- 1,339 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase, cytosolic
- EC
- 1.2.1.12
- UniProt
- Q0J8A4
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, B, C | Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12) | protein | 335 | 23% helix, 23% strand | Q0J8A4 |
| A | Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12) | protein | 334 | 26% helix, 23% strand | Q0J8A4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains O, A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.77 | 0.79 | 110 | SO4 |
| 2 | 1049 | 0.76 | 0.79 | 120 | SO4 |
| 3 | 506 | 0.72 | 0.81 | 55 | empty |
| 4 | 490 | 0.70 | 0.80 | 60 | empty |
| 5 | 55 | 0.66 | 0.95 | 15 | empty |
Interfaces
6 interfaces between chains.
- O–C · 1976 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1968 Ų buried · 32 hydrogen bonds · protein-protein
- O–B · 1459 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1415 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 546 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3E6A · Crystal structure and Functional Analysis of Glyceraldehyde-3-phosphate Dehydrogenase… · the same entry in another collection · chain C against C, TM-score 1.00
- Q0J8A4 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase 1… · a predicted model of the same protein · chain A 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 Q0J8A4
- Elsewhere: RCSB PDB 3E6A · PDBe 3E6A · UniProt Q0J8A4
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