MolNFT v1 · #31263 · protein
Crystal structure of N-acetylglucosaminyltransferase I in complex with udp-glcnac phosphonate
2APC · Alpha-1,3-mannosyl-glycoprotein 2-beta-N…: “Crystal structure of N-acetylglucosaminyltransferase I in complex with udp-glcnac phosphonate”. X-ray diffraction, 2 ligands (UDM, MN), 3 pockets (best druggability 0.77). MolNFT v1 #31263…
- PDB
- 2APC
- Type
- protein
- Length
- 342 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,3-mannosyl-glycoprotein 2-beta-N- acetylglucosaminyltransferase
- EC
- 2.4.1.101
- UniProt
- P27115
- Ligands
- UDM, MN
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,3-mannosyl-glycoprotein 2-beta-N- acetylglucosaminyltransferase (EC 2.4.1.101) | protein | 342 | 36% helix, 20% strand | P27115 |
Ligands and binding sites
- UDM · Uridine-diphosphate-methylene-N-acetyl-glucosamine · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- GOL · Glycerol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.77 | 0.84 | 52 | MN, UDM, GOL |
| 2 | 54 | 0.37 | 0.80 | 17 | GOL |
| 3 | 91 | 0.37 | 0.75 | 15 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2APC · Crystal Structure of N-Acetylglucosaminyltransferase I in Complex with UDP-GlcNAc… · the same entry in another collection · chain A against A, TM-score 1.00
- P27115 · AlphaFold monomer V2.0 prediction for alpha-1,3-mannosyl-glycoprotein… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P27115
- Elsewhere: RCSB PDB 2APC · PDBe 2APC · UniProt P27115
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