MolNFT v1 · #125161 · protein
Human POGLUT1 in complex with factor VII EGF1 and udp
5L0S · Protein O-glucosyltransferase 1: “Human POGLUT1 in complex with factor VII EGF1 and udp”. X-ray diffraction, 4 ligands (UDP, NAG, CA), 6 pockets (best druggability 0.83). MolNFT v1 #125161 on GenesisL1: 3D structure, binding sites…
- PDB
- 5L0S
- Type
- protein
- Length
- 394 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein O-glucosyltransferase 1; Coagulation factor VII
- EC
- 2.4.1.-, 2.4.2.26, 3.4.21.21
- UniProt
- Q8NBL1, P08709
- Ligands
- UDP, NAG, CA, CL
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein O-glucosyltransferase 1 (EC 2.4.1.-, 2.4.2.26) | protein | 355 | 42% helix, 15% strand | Q8NBL1 |
| B | Coagulation factor VII (EC 3.4.21.21) | protein | 39 | 10% helix, 36% strand | P08709 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.83 | 0.97 | 34 | UDP, GOL |
| 2 | 65 | 0.39 | 0.79 | 13 | empty |
| 3 | 87 | 0.39 | 0.77 | 26 | GOL |
| 4 | 72 | 0.32 | 0.75 | 15 | empty |
| 5 | 52 | 0.27 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 827 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5L0S · human POGLUT1 in complex with Factor VII EGF1 and UDP · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NBL1 · AlphaFold monomer V2.0 prediction for protein O-glucosyltransferase 1 (Q8NBL1) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P08709 · AlphaFold monomer V2.0 prediction for coagulation factor VII (P08709) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 Q8NBL1
- Every structure of UniProt P08709
- Elsewhere: RCSB PDB 5L0S · PDBe 5L0S · UniProt Q8NBL1 · UniProt P08709
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