MolNFT v1 · #117857 · protein
Structure of the polyisoprenyl-phosphate glycosyltransferase gtrb (wt)
5EKP · Uncharacterized glycosyltransferase SLL0501: “Structure of the polyisoprenyl-phosphate glycosyltransferase gtrb (wt)”. X-ray diffraction, 2 ligands (UDP, MG), 20 pockets (best druggability 0.77). MolNFT v1 #117857 on GenesisL1: 3D…
- PDB
- 5EKP
- Type
- protein
- Length
- 1,190 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized glycosyltransferase SLL0501
- EC
- 2.4.-.-
- UniProt
- Q55487
- Ligands
- UDP, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Uncharacterized glycosyltransferase SLL0501 (EC 2.4.-.-) | protein | 307 | 49% helix, 13% strand | Q55487 |
| A | Uncharacterized glycosyltransferase SLL0501 (EC 2.4.-.-) | protein | 288 | 48% helix, 16% strand | Q55487 |
| B | Uncharacterized glycosyltransferase SLL0501 (EC 2.4.-.-) | protein | 299 | 51% helix, 16% strand | Q55487 |
| D | Uncharacterized glycosyltransferase SLL0501 (EC 2.4.-.-) | protein | 296 | 47% helix, 15% strand | Q55487 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains C, A, B, D
- MG · Magnesium ion · metal · 4 copies · chains C, A, B, D
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 | 90 | 0.77 | 0.98 | 19 | empty |
| 2 | 667 | 0.69 | 0.77 | 55 | empty |
| 3 | 441 | 0.68 | 0.80 | 55 | empty |
| 4 | 486 | 0.66 | 0.78 | 63 | empty |
| 5 | 366 | 0.62 | 0.78 | 45 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1843 Ų buried · 16 hydrogen bonds · protein-protein
- C–A · 1828 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1796 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1774 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 89 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5EKP · Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB (WT) · the same entry in another collection · chain D against D, TM-score 1.00
- Q55487 · AlphaFold monomer V2.0 prediction for uncharacterized glycosyltransferase SLL0501 (Q55487) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 Q55487
- Elsewhere: RCSB PDB 5EKP · PDBe 5EKP · UniProt Q55487
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