MolNFT v1 · #147642 · protein
Human xylosyltransferase 1 in complex with peptide qeeegsggpqgg
6EJD: “Human xylosyltransferase 1 in complex with peptide qeeegsggpqgg”. X-ray diffraction, 1 ligand (PO4), 4 pockets (best druggability 0.75). MolNFT v1 #147642 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6EJD
- Type
- protein
- Length
- 702 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylosyltransferase 1; Protein ambp
- EC
- 2.4.2.26
- UniProt
- Q86Y38, P02760
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylosyltransferase 1 (EC 2.4.2.26) | protein | 693 | 30% helix, 25% strand | Q86Y38 |
| B | Protein ambp | protein | 9 | 0% helix, 11% strand | P02760 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.75 | 0.79 | 79 | PO4 |
| 2 | 482 | 0.68 | 0.79 | 46 | empty |
| 3 | 105 | 0.45 | 0.79 | 21 | empty |
| 4 | 165 | 0.43 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 615 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 6EJD · Human Xylosyltransferase 1 in complex with peptide QEEEGSGGPQGG · the same entry in another collection · chain A against A, TM-score 1.00
- Q86Y38 · AlphaFold monomer V2.0 prediction for xylosyltransferase 1 (Q86Y38) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P02760 · AlphaFold monomer V2.0 prediction for protein ambp (P02760) · a predicted model of the same protein · chain B against A, TM-score 0.35
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 Q86Y38
- Every structure of UniProt P02760
- Elsewhere: RCSB PDB 6EJD · PDBe 6EJD · UniProt Q86Y38 · UniProt P02760
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