MolNFT v1 · #147636 · protein
Human xylosyltransferase 1 in complex with udp-xylose and peptide qeeegagggqgg
6EJ7: “Human xylosyltransferase 1 in complex with udp-xylose and peptide qeeegagggqgg”. X-ray diffraction, 4 ligands (UDX, NAG, NA), 9 pockets (best druggability 0.75). MolNFT v1 #147636 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6EJ7
- Type
- protein
- Length
- 716 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
- UDX, NAG, NA, PO4
- Pockets
- 9 · 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 | 706 | 30% helix, 25% strand | Q86Y38 |
| B | Protein ambp | protein | 10 | 0% helix, 10% strand | P02760 |
Ligands and binding sites
- UDX · Uridine-5'-diphosphate-xylopyranose · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · 9 copies · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.75 | 0.79 | 76 | UDX, PO4 |
| 2 | 482 | 0.69 | 0.79 | 42 | EDO |
| 3 | 103 | 0.44 | 0.78 | 21 | PO4 |
| 4 | 157 | 0.44 | 0.75 | 24 | PEG |
| 5 | 75 | 0.37 | 0.77 | 15 | EDO |
Interfaces
1 interface between chains.
- A–B · 708 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6EJ7 · Human Xylosyltransferase 1 in complex with UDP-xylose and peptide QEEEGAGGGQGG · 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 0.36
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 6EJ7 · PDBe 6EJ7 · UniProt Q86Y38 · UniProt P02760
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