MolNFT v2 · #159258 · protein
Crystal Structure of Glyceraldehyde-3-phosphate Dehydrogenase from Naegleria fowleri with bound NAD
6NLX: “Crystal Structure of Glyceraldehyde-3-phosphate Dehydrogenase from Naegleria fowleri with bound NAD”. X-ray diffraction at 1.8, 1 ligand (NAD), 11 pockets (best druggability 0.77). MolNFT v2 #159258 on GenesisL1: 3D structure…
- PDB
- 6NLX
- Type
- protein
- Length
- 1,337 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Naegleria fowleri
- Molecule
- Glyceraldehyde-3-phosphate Dehydrogenase
- Ligands
- NAD
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.8 · 4 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glyceraldehyde-3-phosphate Dehydrogenase | protein | 337 | 29% helix, 26% strand | — |
| B | Glyceraldehyde-3-phosphate Dehydrogenase | protein | 333 | 31% helix, 26% strand | — |
| C | Glyceraldehyde-3-phosphate Dehydrogenase | protein | 335 | 31% helix, 27% strand | — |
| D | Glyceraldehyde-3-phosphate Dehydrogenase | protein | 332 | 31% helix, 26% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains B, C, A, D
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.77 | 0.95 | 28 | empty |
| 2 | 408 | 0.72 | 0.83 | 62 | EDO |
| 3 | 462 | 0.72 | 0.82 | 65 | EDO |
| 4 | 642 | 0.70 | 0.78 | 76 | NAD |
| 5 | 610 | 0.69 | 0.78 | 65 | NAD |
Interfaces
6 interfaces between chains.
- A–B · 1967 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1959 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1452 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 1396 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 551 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6NLX · Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from naegleria fowleri with… · 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
- Elsewhere: RCSB PDB 6NLX · PDBe 6NLX
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.