MolNFT v1 · #171155 · protein
Mannosyltransferase pcmangt from pyrobaculum calidifontis in complex with GDP and MN2+
6YV8 · Glycosyl transferase, family 2: “Mannosyltransferase pcmangt from pyrobaculum calidifontis in complex with GDP and MN2+”. X-ray diffraction, 2 ligands (GDP, MN), 8 pockets (best druggability 0.77). MolNFT v1 #171155 on GenesisL1: 3D…
- PDB
- 6YV8
- 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
- GDP, MN
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl transferase, family 2 | protein | 346 | 54% helix, 12% strand | A3MTD6 |
| B | Glycosyl transferase, family 2 | protein | 345 | 54% helix, 13% strand | A3MTD6 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · 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 | 656 | 0.77 | 0.83 | 65 | GDP, MN |
| 2 | 633 | 0.76 | 0.82 | 64 | GDP, MN |
| 3 | 757 | 0.70 | 0.76 | 71 | empty |
| 4 | 734 | 0.68 | 0.75 | 67 | empty |
| 5 | 57 | 0.56 | 0.89 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 940 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6YV8 · Mannosyltransferase PcManGT from Pyrobaculum calidifontis in complex with GDP 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 6YV8 · PDBe 6YV8 · UniProt A3MTD6
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