Research workbench
Mouse POFUT1 in complex with GDP
Analyse Mouse POFUT1 in complex with GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KXQ
- Type
- protein
- Length
- 1,300 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-fucose protein O-fucosyltransferase 1
- EC
- 2.4.1.221
- UniProt
- Q91ZW2
- Ligands
- GDP, NAG, NA
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-fucose protein O-fucosyltransferase 1 (EC 2.4.1.221) | protein | 327 | 42% helix, 17% strand | Q91ZW2 |
| B | GDP-fucose protein O-fucosyltransferase 1 (EC 2.4.1.221) | protein | 325 | 42% helix, 17% strand | Q91ZW2 |
| C | GDP-fucose protein O-fucosyltransferase 1 (EC 2.4.1.221) | protein | 323 | 43% helix, 17% strand | Q91ZW2 |
| D | GDP-fucose protein O-fucosyltransferase 1 (EC 2.4.1.221) | protein | 325 | 41% helix, 17% strand | Q91ZW2 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.84 | 0.85 | 107 | empty |
| 2 | 781 | 0.82 | 0.85 | 94 | empty |
| 3 | 231 | 0.71 | 0.86 | 27 | empty |
| 4 | 295 | 0.61 | 0.79 | 37 | GDP |
| 5 | 245 | 0.59 | 0.80 | 31 | GDP |
Interfaces
3 interfaces between chains.
- C–D · 1314 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1236 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 662 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
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 Q91ZW2
- Elsewhere: RCSB PDB 5KXQ · PDBe 5KXQ · UniProt Q91ZW2
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