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Orthorhombic crystal form of BOGT6A E192Q in complex with udp-galnac, udp, galnac
Analyse Orthorhombic crystal form of BOGT6A E192Q in complex with udp-galnac, udp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CJC
- Type
- protein
- Length
- 955 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
- UD2, UDP, A2G
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyltransferase family 6 (EC 2.4.1.40) | protein | 241 | 29% helix, 20% strand | A7LVT2 |
| B | Glycosyltransferase family 6 (EC 2.4.1.40) | protein | 238 | 29% helix, 23% strand | A7LVT2 |
| C | Glycosyltransferase family 6 (EC 2.4.1.40) | protein | 240 | 30% helix, 21% strand | A7LVT2 |
| D | Glycosyltransferase family 6 (EC 2.4.1.40) | protein | 236 | 28% helix, 19% strand | A7LVT2 |
Ligands and binding sites
- UD2 · Uridine-diphosphate-N-acetylgalactosamine · ligand · 2 copies · chains A, C
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains B, D
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.80 | 0.81 | 79 | empty |
| 2 | 92 | 0.78 | 0.98 | 20 | empty |
| 3 | 594 | 0.75 | 0.82 | 44 | UD2 |
| 4 | 783 | 0.75 | 0.79 | 72 | UD2 |
| 5 | 632 | 0.74 | 0.80 | 69 | UDP, A2G |
Interfaces
6 interfaces between chains.
- C–D · 548 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 527 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 501 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 374 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 238 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4CJC · orthorhombic crystal form of Bogt6a E192Q in complex with UDP-GalNAc, UDP, 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 4CJC · PDBe 4CJC · UniProt A7LVT2
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