Research workbench
Crystal structure of a GDP-L-fucose synthetase from naegleria fowleri bound to NADP
Analyse Crystal structure of a GDP-L-fucose synthetase from naegleria fowleri bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AQZ
- Type
- protein
- Length
- 1,949 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-L-fucose synthetase
- Ligands
- NAP
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | GDP-L-fucose synthetase | protein | 334 | 45% helix, 16% strand | — |
| B | GDP-L-fucose synthetase | protein | 323 | 44% helix, 16% strand | — |
| D | GDP-L-fucose synthetase | protein | 324 | 46% helix, 16% strand | — |
| E | GDP-L-fucose synthetase | protein | 313 | 47% helix, 13% strand | — |
| F | GDP-L-fucose synthetase | protein | 321 | 45% helix, 17% strand | — |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 5 copies · chains A, B, C, E, F
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.76 | 0.79 | 85 | NAP |
| 2 | 843 | 0.76 | 0.80 | 79 | NAP |
| 3 | 961 | 0.76 | 0.78 | 80 | NAP |
| 4 | 960 | 0.75 | 0.78 | 91 | empty |
| 5 | 563 | 0.71 | 0.79 | 54 | NAP |
Interfaces
7 interfaces between chains.
- A–B · 1184 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1175 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 1097 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 377 Ų buried · 0 hydrogen bonds · protein-protein
- B–F · 282 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6AQZ · Crystal structure of a gdp-l-fucose synthetase from Naegleria fowleri bound to NADP · 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 6AQZ · PDBe 6AQZ
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