MolNFT v1 · #119829 · protein
Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with man-beta-pnp
5GGK · Protein O-linked-mannose beta-1,2-N…: “Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in…”. X-ray diffraction, 1 ligand (MBE), 2 pockets (best druggability 0.44). MolNFT v1…
- PDB
- 5GGK
- Type
- protein
- Length
- 305 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein O-linked-mannose beta-1,2-N- acetylglucosaminyltransferase 1
- EC
- 2.4.1.-
- UniProt
- Q8WZA1
- Ligands
- MBE
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein O-linked-mannose beta-1,2-N- acetylglucosaminyltransferase 1 (EC 2.4.1.-) | protein | 153 | 15% helix, 41% strand | Q8WZA1 |
| B | Protein O-linked-mannose beta-1,2-N- acetylglucosaminyltransferase 1 (EC 2.4.1.-) | protein | 152 | 15% helix, 41% strand | Q8WZA1 |
Ligands and binding sites
- MBE · 4-nitrophenyl beta-D-mannopyranoside · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.44 | 0.83 | 16 | empty |
| 2 | 158 | 0.43 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 433 Ų buried · 5 hydrogen bonds · protein-protein
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 Q8WZA1
- Elsewhere: RCSB PDB 5GGK · PDBe 5GGK · UniProt Q8WZA1
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