Research workbench
Crystal structure of human protein O-mannose beta-1,2-N- acetylglucosaminyltransferase form II
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
- 5GGF
- Type
- protein
- Length
- 1,607 residues
- Chains
- 3
- 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
- Pockets
- 17 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 26% 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 | 535 | 28% helix, 27% strand | Q8WZA1 |
| B, C | Protein O-linked-mannose beta-1,2-N- acetylglucosaminyltransferase 1 (EC 2.4.1.-) | protein | 536 | 26% helix, 25% strand | Q8WZA1 |
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.71 | 0.77 | 78 | empty |
| 2 | 708 | 0.65 | 0.74 | 79 | empty |
| 3 | 369 | 0.60 | 0.76 | 47 | empty |
| 4 | 369 | 0.55 | 0.74 | 40 | empty |
| 5 | 253 | 0.51 | 0.75 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–B · 729 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 348 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 240 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 5GGF · Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase… · 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 B against A, TM-score 0.97
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 5GGF · PDBe 5GGF · UniProt Q8WZA1
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