Research workbench
Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from pyrococcus horikoshii OT3
Analyse Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from pyrococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CZC
- Type
- protein
- Length
- 1,332 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.59
- UniProt
- O59494
- Ligands
- NAD, PO4
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.59) | protein | 334 | 39% helix, 25% strand | O59494 |
| B, C | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.59) | protein | 333 | 38% helix, 25% strand | O59494 |
| D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.59) | protein | 332 | 38% helix, 25% strand | O59494 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.76 | 0.97 | 30 | empty |
| 2 | 90 | 0.74 | 0.97 | 24 | empty |
| 3 | 706 | 0.68 | 0.76 | 76 | PO4, NAD |
| 4 | 673 | 0.66 | 0.76 | 80 | PO4, NAD |
| 5 | 681 | 0.66 | 0.75 | 62 | PO4, NAD |
Interfaces
6 interfaces between chains.
- B–C · 1859 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1846 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1503 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1484 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 475 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2CZC · Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Pyrococcus horikoshii… · the same entry in another collection · chain D against D, TM-score 1.00
- O59494 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (O59494) · a predicted model of the same protein · chain B 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 O59494
- Elsewhere: RCSB PDB 2CZC · PDBe 2CZC · UniProt O59494
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