Research workbench
Orthorhombic crystal form of BOGT6A E192Q in complex with galnac
Analyse Orthorhombic crystal form of BOGT6A E192Q in complex with galnac in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CJB
- Type
- protein
- Length
- 944 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyltransferase family 6
- EC
- 2.4.1.40
- UniProt
- A7LVT2
- Ligands
- A2G
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycosyltransferase family 6 (EC 2.4.1.40) | protein | 236 | 32% helix, 22% strand | A7LVT2 |
| C | Glycosyltransferase family 6 (EC 2.4.1.40) | protein | 237 | 32% helix, 23% strand | A7LVT2 |
| D | Glycosyltransferase family 6 (EC 2.4.1.40) | protein | 235 | 31% helix, 22% strand | A7LVT2 |
Ligands and binding sites
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.82 | 0.84 | 91 | empty |
| 2 | 980 | 0.74 | 0.77 | 84 | A2G |
| 3 | 604 | 0.74 | 0.81 | 77 | A2G |
| 4 | 229 | 0.63 | 0.82 | 31 | A2G |
| 5 | 227 | 0.48 | 0.74 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–B · 508 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 497 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 487 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 309 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 213 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4CJB · orthorhombic crystal form of Bogt6a E192Q in complex with GalNAc · the same entry in another collection · 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 A7LVT2
- Elsewhere: RCSB PDB 4CJB · PDBe 4CJB · UniProt A7LVT2
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