MolNFT v1 · #21267 · protein
Crystal structure of yeast ALPHA1,2-mannosyltransferase KRE2P/MNT1P: binary complex with GDP/MN
1S4O · Glycolipid 2-alpha-mannosyltransferase: “Crystal structure of yeast ALPHA1,2-mannosyltransferase KRE2P/MNT1P: binary complex with GDP/MN”. X-ray diffraction, 7 ligands (GDP, MAN, NAG), 2 pockets (best druggability 0.89). MolNFT v1…
- PDB
- 1S4O
- Type
- protein
- Length
- 670 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycolipid 2-alpha-mannosyltransferase
- EC
- 2.4.1.131
- UniProt
- P27809
- Ligands
- GDP, MAN, NAG, NDG, BMA, MN, CL
- Pockets
- 2 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycolipid 2-alpha-mannosyltransferase (EC 2.4.1.131) | protein | 335 | 46% helix, 13% strand | P27809 |
| B | Glycolipid 2-alpha-mannosyltransferase (EC 2.4.1.131) | protein | 335 | 47% helix, 13% strand | P27809 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.89 | 0.90 | 112 | MN, GDP, EPE, CL |
| 2 | 128 | 0.40 | 0.74 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1449 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1S4O · Crystal structure of yeast alpha1,2-mannosyltransferase Kre2p/Mnt1p: binary complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P27809 · AlphaFold monomer V2.0 prediction for glycolipid 2-alpha- mannosyltransferase (P27809) · a predicted model of the same protein · chain B 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 P27809
- Elsewhere: RCSB PDB 1S4O · PDBe 1S4O · UniProt P27809
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