MolNFT v1 · #35907 · protein
Structural study of project id AQ_1065 from aquifex aeolicus VF5
2EP7 · Glyceraldehyde-3-phosphate dehydrogenase: “Structural study of project id AQ_1065 from aquifex aeolicus VF5”. X-ray diffraction, 1 ligand (NAD), 6 pockets (best druggability 0.69). MolNFT v1 #35907 on GenesisL1: 3D structure…
- PDB
- 2EP7
- Type
- protein
- Length
- 677 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
- UniProt
- O67161
- Ligands
- NAD
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 338 | 31% helix, 28% strand | O67161 |
| B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 339 | 29% helix, 28% strand | O67161 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.69 | 0.80 | 41 | NAD |
| 2 | 535 | 0.68 | 0.78 | 51 | NAD |
| 3 | 62 | 0.34 | 0.77 | 16 | empty |
| 4 | 71 | 0.33 | 0.75 | 15 | empty |
| 5 | 66 | 0.29 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1923 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 2EP7 · Structural study of Project ID aq_1065 from Aquifex aeolicus VF5 · the same entry in another collection · chain A against A, TM-score 1.00
- O67161 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (O67161) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O67161
- Elsewhere: RCSB PDB 2EP7 · PDBe 2EP7 · UniProt O67161
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