MolNFT v1 · #16861 · protein
The crystal structure of glyceraldehyde 3-phosphate dehydrogenase from alcaligenes xylosoxidans at 1.7 a resolution.
1OBF: “The crystal structure of glyceraldehyde 3-phosphate dehydrogenase from alcaligenes xylosoxidans at 1.7 a…”. X-ray diffraction, 2 ligands (K, SO4), 3 pockets (best druggability 0.62). MolNFT v1 #16861 on GenesisL1: 3D structure…
- PDB
- 1OBF
- Type
- protein
- Length
- 670 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde 3-phosphate dehydrogenase
- EC
- 1.2.1.12
- Ligands
- K, SO4
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, P | Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 335 | 30% helix, 28% strand | — |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains O, P
- SO4 · Sulfate ion · ion · 3 copies · chains O, P
- PG4 · Tetraethylene glycol · additive · chains P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.62 | 0.76 | 54 | SO4 |
| 2 | 372 | 0.59 | 0.76 | 48 | SO4 |
| 3 | 56 | 0.29 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- O–P · 2021 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 1OBF · The crystal structure of Glyceraldehyde 3-phosphate Dehydrogenase from Alcaligenes… · the same entry in another collection · chain O against O, 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
- Elsewhere: RCSB PDB 1OBF · PDBe 1OBF
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