Research workbench
Crystal structure of human protein O-mannose beta-1,2-N- acetylglucosaminyltransferase in complex with mn, udp and mannosyl- peptide
Analyse Crystal structure of human protein O-mannose beta-1,2-N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GGI
- Type
- protein
- Length
- 959 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; Mannosyl-peptide
- EC
- 2.4.1.-
- UniProt
- Q8WZA1
- Ligands
- UDP, ACE, MAN, MN, PO4
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 22% 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 | 394 | 34% helix, 19% strand | Q8WZA1 |
| B | Protein O-linked-mannose beta-1,2-N- acetylglucosaminyltransferase 1 (EC 2.4.1.-) | protein | 551 | 28% helix, 25% strand | Q8WZA1 |
| F | Mannosyl-peptide | protein | 9 | 0% helix, 0% strand | — |
| G | Mannosyl-peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- ACE · Acetyl group · ligand · chains A, F
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B, F, G
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.80 | 0.87 | 51 | UDP, MN, MAN |
| 2 | 488 | 0.75 | 0.83 | 44 | UDP, MN |
| 3 | 269 | 0.60 | 0.79 | 30 | MAN |
| 4 | 397 | 0.56 | 0.73 | 38 | empty |
| 5 | 271 | 0.53 | 0.75 | 27 | empty |
Interfaces
4 interfaces between chains.
- B–G · 317 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 308 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 305 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 263 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan, 1 covalent (disulfide, O-glycosylation, covalent ligand).
Compared structures
- 5GGI · Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in… · 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
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 5GGI · PDBe 5GGI · UniProt Q8WZA1
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