Research workbench
Crystal structure of murine N-acetylglucosaminyl transferase iva (gnt- iva) lectin domain in unliganded form
Analyse Crystal structure of murine N-acetylglucosaminyl transferase iva (gnt- iva)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VMT
- Type
- protein
- Length
- 859 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,3-mannosyl-glycoprotein 4-beta-N- acetylglucosaminyltransferase a soluble form
- UniProt
- Q812G0
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,3-mannosyl-glycoprotein 4-beta-N- acetylglucosaminyltransferase a soluble form | protein | 140 | 8% helix, 46% strand | Q812G0 |
| B | Alpha-1,3-mannosyl-glycoprotein 4-beta-N- acetylglucosaminyltransferase a soluble form | protein | 146 | 8% helix, 45% strand | Q812G0 |
| C | Alpha-1,3-mannosyl-glycoprotein 4-beta-N- acetylglucosaminyltransferase a soluble form | protein | 139 | 6% helix, 47% strand | Q812G0 |
| D | Alpha-1,3-mannosyl-glycoprotein 4-beta-N- acetylglucosaminyltransferase a soluble form | protein | 145 | 9% helix, 45% strand | Q812G0 |
| E | Alpha-1,3-mannosyl-glycoprotein 4-beta-N- acetylglucosaminyltransferase a soluble form | protein | 144 | 6% helix, 45% strand | Q812G0 |
| F | Alpha-1,3-mannosyl-glycoprotein 4-beta-N- acetylglucosaminyltransferase a soluble form | protein | 145 | 8% helix, 45% strand | Q812G0 |
Ligands and binding sites
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.81 | 0.82 | 106 | empty |
| 2 | 207 | 0.46 | 0.74 | 26 | empty |
| 3 | 56 | 0.40 | 0.81 | 15 | empty |
| 4 | 67 | 0.34 | 0.76 | 17 | empty |
| 5 | 83 | 0.30 | 0.72 | 15 | empty |
Interfaces
9 interfaces between chains.
- D–F · 465 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 457 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 281 Ų buried · 1 hydrogen bond · protein-protein
- C–E · 262 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 203 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7VMT · Crystal structure of murine N-acetylglucosaminyl transferase IVa (GnT-IVa) lectin domain… · the same entry in another collection · chain F against F, TM-score 1.00
- Q812G0 · AlphaFold monomer V2.0 prediction for alpha-1,3-mannosyl-glycoprotein… · a predicted model of the same protein · chain A 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 Q812G0
- Elsewhere: RCSB PDB 7VMT · PDBe 7VMT · UniProt Q812G0
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