Research workbench
Mannosyltransferase pcmangt from pyrobaculum calidifontis in complex with GDP-man and MN2+
Analyse Mannosyltransferase pcmangt from pyrobaculum calidifontis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YV9
- Type
- protein
- Length
- 691 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl transferase, family 2
- UniProt
- A3MTD6
- Ligands
- GDD, MN
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl transferase, family 2 | protein | 345 | 53% helix, 12% strand | A3MTD6 |
| B | Glycosyl transferase, family 2 | protein | 346 | 54% helix, 13% strand | A3MTD6 |
Ligands and binding sites
- GDD · Guanosine-5'-diphosphate-alpha-D-mannose · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.79 | 0.84 | 59 | GDD, MN |
| 2 | 652 | 0.77 | 0.83 | 66 | GDD, MN |
| 3 | 896 | 0.72 | 0.76 | 80 | empty |
| 4 | 717 | 0.69 | 0.76 | 59 | empty |
| 5 | 62 | 0.56 | 0.88 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1044 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6YV9 · Mannosyltransferase PcManGT from Pyrobaculum calidifontis in complex with GDP-Man and Mn2+ · 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 A3MTD6
- Elsewhere: RCSB PDB 6YV9 · PDBe 6YV9 · UniProt A3MTD6
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