MolNFT v1 · #112932 · protein
X-ray structure of the mannosyltransferase KTR4P from S. cerevisiae in complex with GDP
5A07 · Probable mannosyltransferase KTR4: “X-ray structure of the mannosyltransferase KTR4P from S. cerevisiae in complex with GDP”. X-ray diffraction, 2 ligands (GDP, MN), 5 pockets (best druggability 0.78). MolNFT v1 #112932 on…
- PDB
- 5A07
- Type
- protein
- Length
- 789 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable mannosyltransferase KTR4
- EC
- 2.4.1.-
- UniProt
- P38131
- Ligands
- GDP, MN
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable mannosyltransferase KTR4 (EC 2.4.1.-) | protein | 395 | 46% helix, 12% strand | P38131 |
| B | Probable mannosyltransferase KTR4 (EC 2.4.1.-) | protein | 394 | 45% helix, 12% strand | P38131 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.78 | 0.83 | 75 | empty |
| 2 | 474 | 0.68 | 0.79 | 43 | GDP, MN |
| 3 | 449 | 0.66 | 0.79 | 43 | GDP, MN |
| 4 | 80 | 0.46 | 0.81 | 19 | empty |
| 5 | 57 | 0.39 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 830 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5A07 · X-ray structure of the mannosyltransferase Ktr4p from S. cerevisiae in complex with GDP · the same entry in another collection · chain A against A, TM-score 1.00
- P38131 · AlphaFold monomer V2.0 prediction for probable mannosyltransferase KTR4 (P38131) · a predicted model of the same protein · 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 P38131
- Elsewhere: RCSB PDB 5A07 · PDBe 5A07 · UniProt P38131
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