Research workbench
Crystal structure of pectin methylesterase D178A mutant in complex with hexasaccharide III
Analyse Crystal structure of pectin methylesterase D178A mutant 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
- 2NT6
- Type
- protein
- Length
- 684 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pectinesterase a
- EC
- 3.1.1.11
- UniProt
- P0C1A9
- Ligands
- M8C, ADA
- Pockets
- 4 · best druggability 0.39
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pectinesterase a (EC 3.1.1.11) | protein | 342 | 9% helix, 39% strand | P0C1A9 |
Ligands and binding sites
- M8C · methyl alpha-D-galactopyranuronate · ligand · 4 copies · chains A, B
- ADA · alpha-D-galactopyranuronic acid · sugar · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.39 | 0.75 | 21 | empty |
| 2 | 92 | 0.37 | 0.75 | 18 | M8C, ADA |
| 3 | 88 | 0.36 | 0.75 | 15 | empty |
| 4 | 92 | 0.35 | 0.74 | 20 | M8C, ADA |
Interfaces
1 interface between chains.
- A–B · 304 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2NT6 · Crystal structure of pectin methylesterase D178A mutant in complex with hexasaccharide III · the same entry in another collection · chain A against A, TM-score 1.00
- P0C1A9 · AlphaFold monomer V2.0 prediction for pectinesterase a (P0C1A9) · 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 P0C1A9
- Elsewhere: RCSB PDB 2NT6 · PDBe 2NT6 · UniProt P0C1A9
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