MolNFT v1 · #27080 · protein
Crystal structure of a pectin methylesterase inhibitor from arabidopsis thaliana
1X8Z · INVERTASE/PECTIN methylesterase inhibitor family protein: “Crystal structure of a pectin methylesterase inhibitor from arabidopsis thaliana”. X-ray diffraction, 2 pockets (best druggability 0.66). MolNFT v1 #27080 on GenesisL1: 3D…
- PDB
- 1X8Z
- Type
- protein
- Length
- 448 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- INVERTASE/PECTIN methylesterase inhibitor family protein
- UniProt
- Q9LNF2
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | INVERTASE/PECTIN methylesterase inhibitor family protein | protein | 151 | 81% helix, 0% strand | Q9LNF2 |
| B | INVERTASE/PECTIN methylesterase inhibitor family protein | protein | 147 | 76% helix, 0% strand | Q9LNF2 |
| C | INVERTASE/PECTIN methylesterase inhibitor family protein | protein | 150 | 75% helix, 0% strand | Q9LNF2 |
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 | 433 | 0.66 | 0.79 | 46 | empty |
| 2 | 99 | 0.34 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1379 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 528 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 324 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1X8Z · Crystal structure of a pectin methylesterase inhibitor from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- Q9LNF2 · AlphaFold monomer V2.0 prediction for pectinesterase inhibitor 1 (Q9LNF2) · a predicted model of the same protein · chain B against A, TM-score 0.83
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 Q9LNF2
- Elsewhere: RCSB PDB 1X8Z · PDBe 1X8Z · UniProt Q9LNF2
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