Research workbench
Structure of a glycosomal glyceraldehyde 3-phosphate dehydrogenase from trypanosoma brucei
Analyse Structure of a glycosomal glyceraldehyde 3-phosphate dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P8R
- Type
- protein
- Length
- 1,323 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
- Q38AR9
- Ligands
- NAD, MG
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Glyceraldehyde 3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12) | protein | 331 | 30% helix, 28% strand | Q38AR9 |
| C | Glyceraldehyde 3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12) | protein | 330 | 30% helix, 28% strand | Q38AR9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.82 | 0.84 | 111 | empty |
| 2 | 1140 | 0.77 | 0.79 | 114 | NAD |
| 3 | 579 | 0.71 | 0.79 | 55 | NAD |
| 4 | 562 | 0.71 | 0.79 | 59 | NAD |
| 5 | 75 | 0.35 | 0.76 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2050 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 2043 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1385 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1382 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 562 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4P8R · Structure of a glycosomal glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma brucei · the same entry in another collection · chain A 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 Q38AR9
- Elsewhere: RCSB PDB 4P8R · PDBe 4P8R · UniProt Q38AR9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.