MolNFT v1 · #177160 · protein
Crystal structure of POMGNT2 in complex with udp
7E9J · Protein O-linked-mannose beta-1,4-N…: “Crystal structure of POMGNT2 in complex with udp”. X-ray diffraction, 2 ligands (UDP, NAG), 15 pockets (best druggability 0.68). MolNFT v1 #177160 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7E9J
- Type
- protein
- Length
- 1,042 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein O-linked-mannose beta-1,4-N- acetylglucosaminyltransferase 2
- EC
- 2.4.1.312
- UniProt
- Q5NDF2
- Ligands
- UDP, NAG
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein O-linked-mannose beta-1,4-N- acetylglucosaminyltransferase 2 (EC 2.4.1.312) | protein | 521 | 27% helix, 27% strand | Q5NDF2 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.68 | 0.80 | 40 | UDP |
| 2 | 413 | 0.67 | 0.79 | 39 | UDP |
| 3 | 390 | 0.63 | 0.78 | 41 | empty |
| 4 | 386 | 0.62 | 0.77 | 41 | empty |
| 5 | 189 | 0.61 | 0.83 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 3017 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
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 Q5NDF2
- Elsewhere: RCSB PDB 7E9J · PDBe 7E9J · UniProt Q5NDF2
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