Research workbench
Monocot chimeric jacalin JAC1 from oryza sativa: dirigent domain (crystal form 2)
Analyse Monocot chimeric jacalin JAC1 from oryza sativa: dirigent domain (crystal form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7YWE
- Type
- protein
- Length
- 432 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dirigent protein
- UniProt
- Q306J3
- Ligands
- PO4
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dirigent protein | protein | 138 | 2% helix, 53% strand | Q306J3 |
| B | Dirigent protein | protein | 152 | 2% helix, 60% strand | Q306J3 |
| C | Dirigent protein | protein | 142 | 2% helix, 63% strand | Q306J3 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.73 | 0.86 | 33 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1514 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 921 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 895 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7YWE · Monocot chimeric jacalin JAC1 from Oryza sativa: dirigent domain (crystal form 2) · 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 Q306J3
- Elsewhere: RCSB PDB 7YWE · PDBe 7YWE · UniProt Q306J3
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