Research workbench
Tarp-udp-glcnac-mg
Analyse Tarp-udp-glcnac-mg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H2N
- Type
- protein
- Length
- 936 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ss-1,3-N-acetylglucosaminyltransferase
- UniProt
- A0A0H3JNB0
- Ligands
- UD1, MG, CL
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ss-1,3-N-acetylglucosaminyltransferase | protein | 312 | 45% helix, 15% strand | A0A0H3JNB0 |
| B | Probable ss-1,3-N-acetylglucosaminyltransferase | protein | 313 | 46% helix, 15% strand | A0A0H3JNB0 |
| C | Probable ss-1,3-N-acetylglucosaminyltransferase | protein | 311 | 46% helix, 14% strand | A0A0H3JNB0 |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 5 copies · chains A, B, C
- CL · Chloride ion · ion · 20 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.60 | 0.84 | 22 | empty |
| 2 | 173 | 0.58 | 0.82 | 23 | CL |
| 3 | 175 | 0.58 | 0.81 | 21 | empty |
| 4 | 304 | 0.52 | 0.74 | 42 | UD1, CL |
| 5 | 248 | 0.48 | 0.74 | 37 | UD1, CL |
Interfaces
3 interfaces between chains.
- B–C · 477 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 450 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 439 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6H2N · TarP-UDP-GlcNAc-Mg · the same entry in another collection · chain B against B, 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 A0A0H3JNB0
- Elsewhere: RCSB PDB 6H2N · PDBe 6H2N · UniProt A0A0H3JNB0
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