MolNFT v1 · #161143 · protein
Structure of an inactive variant (D94N) of mpt-2, a GDP-man-dependent mannosyltransferase from leishmania mexicana, in complex with beta-1, 2-mannobiose
6Q4Z · Lmxm mpt-2 D94N: “Structure of an inactive variant (D94N) of mpt-2, a GDP-man-dependent mannosyltransferase from leishmania…”. X-ray diffraction, 2 ligands (MAN, BMA), 8 pockets (best druggability 0.72). MolNFT v1 #161143 on…
- PDB
- 6Q4Z
- Type
- protein
- Length
- 611 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lmxm mpt-2 D94N
- UniProt
- E9AND8
- Ligands
- MAN, BMA
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lmxm mpt-2 D94N | protein | 310 | 9% helix, 51% strand | E9AND8 |
| B | Lmxm mpt-2 D94N | protein | 301 | 6% helix, 54% strand | E9AND8 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.72 | 0.91 | 30 | empty |
| 2 | 330 | 0.63 | 0.79 | 38 | MAN, BMA |
| 3 | 87 | 0.60 | 0.88 | 20 | empty |
| 4 | 252 | 0.55 | 0.77 | 29 | MAN, BMA |
| 5 | 134 | 0.49 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1364 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 6Q4Z · Structure of an inactive variant (D94N) of MPT-2, a GDP-Man-dependent mannosyltransferase… · 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 E9AND8
- Elsewhere: RCSB PDB 6Q4Z · PDBe 6Q4Z · UniProt E9AND8
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