MolNFT v1 · #117846 · protein
Structure of the polyisoprenyl-phosphate glycosyltransferase gtrb (F215A mutant)
5EKE · Uncharacterized glycosyltransferase SLL0501: “Structure of the polyisoprenyl-phosphate glycosyltransferase gtrb (F215A mutant)”. X-ray diffraction, 2 ligands (UDP, MG), 19 pockets (best druggability 0.76). MolNFT v1 #117846 on…
- PDB
- 5EKE
- 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
- 19 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized glycosyltransferase SLL0501 (EC 2.4.-.-) | protein | 288 | 48% helix, 16% strand | Q55487 |
| B | Uncharacterized glycosyltransferase SLL0501 (EC 2.4.-.-) | protein | 299 | 49% helix, 15% strand | Q55487 |
| C | Uncharacterized glycosyltransferase SLL0501 (EC 2.4.-.-) | protein | 307 | 50% helix, 15% strand | Q55487 |
| D | Uncharacterized glycosyltransferase SLL0501 (EC 2.4.-.-) | protein | 296 | 48% helix, 15% strand | Q55487 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.76 | 0.78 | 116 | UDP |
| 2 | 603 | 0.70 | 0.78 | 72 | empty |
| 3 | 136 | 0.68 | 0.89 | 31 | empty |
| 4 | 446 | 0.68 | 0.79 | 52 | empty |
| 5 | 601 | 0.65 | 0.75 | 63 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1884 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1860 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1799 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1763 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 93 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5EKE · Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB (F215A mutant) · 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 5EKE · PDBe 5EKE · UniProt Q55487
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