MolNFT v1 · #108912 · protein
Crystal structure of mouse xyloside xylosyltransferase 1 complexed with acceptor ligand
4WM0: “Crystal structure of mouse xyloside xylosyltransferase 1 complexed with acceptor ligand”. X-ray diffraction, 2 ligands (BGC, XYS), 1 pocket (best druggability 0.76). MolNFT v1 #108912 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4WM0
- Type
- protein
- Length
- 334 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xyloside xylosyltransferase 1; Coagulation factor IX
- EC
- 2.4.2.-, 3.4.21.22
- UniProt
- Q3U4G3, P00740
- Ligands
- BGC, XYS
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xyloside xylosyltransferase 1 (EC 2.4.2.-) | protein | 299 | 45% helix, 19% strand | Q3U4G3 |
| D | Coagulation factor IX (EC 3.4.21.22) | protein | 35 | 0% helix, 6% strand | P00740 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.76 | 0.81 | 66 | BGC, XYS |
Interfaces
1 interface between chains.
- A–D · 618 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, O-glycosylation).
Compared structures
- 4WM0 · Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with acceptor ligand · the same entry in another collection · chain A against A, TM-score 1.00
- Q3U4G3 · AlphaFold monomer V2.0 prediction for xyloside xylosyltransferase 1 (Q3U4G3) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P00740 · AlphaFold monomer V2.0 prediction for coagulation factor IX (P00740) · a predicted model of the same protein · chain D against A, TM-score 0.42
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 Q3U4G3
- Every structure of UniProt P00740
- Elsewhere: RCSB PDB 4WM0 · PDBe 4WM0 · UniProt Q3U4G3 · UniProt P00740
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