Research workbench
Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from naegleria fowleri with bound NAD
Analyse Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from naegleria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NLX
- Type
- protein
- Length
- 1,337 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- Ligands
- NAD
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 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
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