Research workbench
Crystal structure of taga with udp-glcnac
Analyse Crystal structure of taga with udp-glcnac in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MPK
- Type
- protein
- Length
- 592 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D- mannosaminyltransferase
- EC
- 2.4.1.187
- UniProt
- D3T4E0
- Ligands
- UD1
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D- mannosaminyltransferase (EC 2.4.1.187) | protein | 197 | 46% helix, 18% strand | D3T4E0 |
| B | N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D- mannosaminyltransferase (EC 2.4.1.187) | protein | 198 | 45% helix, 18% strand | D3T4E0 |
| C | N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D- mannosaminyltransferase (EC 2.4.1.187) | protein | 197 | 45% helix, 18% strand | D3T4E0 |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 3 copies · chains A, B, C
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 | 179 | 0.83 | 0.96 | 33 | empty |
| 2 | 169 | 0.46 | 0.76 | 31 | UD1 |
| 3 | 136 | 0.42 | 0.76 | 33 | empty |
| 4 | 121 | 0.37 | 0.74 | 22 | empty |
| 5 | 82 | 0.32 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 491 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 455 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 389 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7MPK · Crystal structure of TagA with UDP-GlcNAc · 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 D3T4E0
- Elsewhere: RCSB PDB 7MPK · PDBe 7MPK · UniProt D3T4E0
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