Research workbench
Thioacylenzyme intermediate of bacillus stearothermophilus phosphorylating GAPDH
Analyse Thioacylenzyme intermediate of bacillus stearothermophilus phosphorylating GAPDH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CMC
- Type
- protein
- Length
- 1,336 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
- P00362
- Ligands
- G3H, NAD, SO4
- Pockets
- 18 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, P, Q, R | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 334 | 30% helix, 30% strand | P00362 |
Ligands and binding sites
- G3H · Glyceraldehyde-3-phosphate · ligand · 4 copies · chains O, P, Q, R
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains O, R, P, Q
- SO4 · Sulfate ion · ion · 18 copies · chains O, P, Q, R
- GOL · Glycerol · additive · 8 copies · chains O, P, R, Q
- EDO · 1,2-ethanediol · additive · chains Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.73 | 0.95 | 22 | empty |
| 2 | 603 | 0.72 | 0.80 | 61 | G3H, SO4, NAD |
| 3 | 495 | 0.71 | 0.81 | 54 | G3H, SO4, NAD |
| 4 | 501 | 0.70 | 0.80 | 50 | G3H, SO4, NAD |
| 5 | 483 | 0.70 | 0.80 | 51 | G3H, SO4, NAD |
Interfaces
6 interfaces between chains.
- O–P · 2085 Ų buried · 37 hydrogen bonds · protein-protein
- Q–R · 2081 Ų buried · 33 hydrogen bonds · protein-protein
- O–R · 1445 Ų buried · 22 hydrogen bonds · protein-protein
- P–Q · 1444 Ų buried · 22 hydrogen bonds · protein-protein
- O–Q · 555 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3CMC · Thioacylenzyme intermediate of Bacillus stearothermophilus phosphorylating GAPDH · 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 3CMC · PDBe 3CMC · UniProt P00362
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