Research workbench
Mouse POFUT1 in complex with mouse factor VII EGF1 and GDP
Analyse Mouse POFUT1 in complex with mouse factor VII EGF1 and GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KXH
- Type
- protein
- Length
- 388 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-fucose protein O-fucosyltransferase 1; Coagulation factor VII
- EC
- 2.4.1.221, 3.4.21.21
- UniProt
- Q91ZW2, P70375
- Ligands
- GDP, NAG
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-fucose protein O-fucosyltransferase 1 (EC 2.4.1.221) | protein | 350 | 41% helix, 16% strand | Q91ZW2 |
| B | Coagulation factor VII (EC 3.4.21.21) | protein | 38 | 8% helix, 37% strand | P70375 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.76 | 0.84 | 46 | GDP |
| 2 | 186 | 0.52 | 0.78 | 34 | empty |
| 3 | 54 | 0.37 | 0.80 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 991 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5KXH · mouse POFUT1 in complex with mouse Factor VII EGF1 and GDP · the same entry in another collection · chain A against A, TM-score 1.00
- Q91ZW2 · AlphaFold monomer V2.0 prediction for GDP-fucose protein O-fucosyltransferase 1 (Q91ZW2) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P70375 · AlphaFold monomer V2.0 prediction for coagulation factor VII (P70375) · a predicted model of the same protein · chain B against A, TM-score 0.89
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
- Every structure of UniProt P70375
- Elsewhere: RCSB PDB 5KXH · PDBe 5KXH · UniProt Q91ZW2 · UniProt P70375
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