MolNFT v1 · #119834 · protein
Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with glcnac- BETA1,2-man-peptide
5GGP · 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, 3 ligands (MAN, NAG, NA), 2 pockets (best druggability 0.64).…
- PDB
- 5GGP
- Type
- protein
- Length
- 314 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein O-linked-mannose beta-1,2-N- acetylglucosaminyltransferase 1; 10-mer peptide from…
- EC
- 2.4.1.-
- UniProt
- Q8WZA1, Q14118
- Ligands
- MAN, NAG, NA
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein O-linked-mannose beta-1,2-N- acetylglucosaminyltransferase 1 (EC 2.4.1.-) | protein | 150 | 15% helix, 41% strand | Q8WZA1 |
| C | 10-mer peptide from dystroglycan | protein | 5 | 0% helix, 0% strand | Q14118 |
| D | 10-mer peptide from dystroglycan | protein | 9 | 0% helix, 0% strand | Q14118 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, C, B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, C, B, D
- NA · Sodium ion · metal · 5 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.64 | 0.78 | 44 | NA |
| 2 | 213 | 0.46 | 0.74 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–B · 390 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 210 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 199 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 glycan (O-glycosylation).
Compared structures
- 5GGP · Crystal structure of N-terminal domain of human protein O-mannose… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8WZA1 · AlphaFold monomer V2.0 prediction for protein O-linked-mannose… · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q14118 · AlphaFold monomer V2.0 prediction for dystroglycan (Q14118) · a predicted model of the same protein · chain C against A, TM-score 0.78
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
- Every structure of UniProt Q14118
- Elsewhere: RCSB PDB 5GGP · PDBe 5GGP · UniProt Q8WZA1 · UniProt Q14118
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