Research workbench
Coenzyme-induced conformational changes in glyceraldehyde-3- phosphate dehydrogenase from bacillus stearothermophillus
Analyse Coenzyme-induced conformational changes in 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
- 2GD1
- Type
- protein
- Length
- 1,336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apo-D-glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.12
- UniProt
- P00362
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, P, Q, R | Apo-D-glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 334 | 32% helix, 28% strand | P00362 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains O, P, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.77 | 0.97 | 28 | empty |
| 2 | 501 | 0.66 | 0.78 | 58 | SO4 |
| 3 | 459 | 0.66 | 0.78 | 64 | SO4 |
| 4 | 452 | 0.65 | 0.78 | 62 | SO4 |
| 5 | 467 | 0.65 | 0.78 | 63 | SO4 |
Interfaces
6 interfaces between chains.
- O–P · 2132 Ų buried · 34 hydrogen bonds · protein-protein
- Q–R · 2129 Ų buried · 37 hydrogen bonds · protein-protein
- O–R · 1427 Ų buried · 13 hydrogen bonds · protein-protein
- P–Q · 1414 Ų buried · 16 hydrogen bonds · protein-protein
- P–R · 575 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2GD1 · Coenzyme-induced conformational changes in glyceraldehyde-3-phosphate dehydrogenase from… · the same entry in another collection · chain R against R, TM-score 1.00
- P00362 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P00362) · a predicted model of the same protein · chain Q 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 P00362
- Elsewhere: RCSB PDB 2GD1 · PDBe 2GD1 · UniProt P00362
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