Research workbench
Cryo-EM structure of plant receptor like protein RXEG1 in complex with xyloglucanase XEG1 and BAK1
Analyse Cryo-EM structure of plant receptor like protein RXEG1 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
- 7DRC
- Type
- protein
- Length
- 1,304 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell 12A endoglucanase; Membrane-localized lrr receptor-like protein; Brassinosteroid…
- UniProt
- Q30BZ2, A0A2I8B6R1
- Ligands
- NAG, BMA, MAN
- Pockets
- 13 · best druggability 0.75
Structure
electron microscopy · 3 distinct chains · 13% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell 12A endoglucanase | protein | 222 | 8% helix, 54% strand | Q30BZ2 |
| C | Membrane-localized lrr receptor-like protein | protein | 906 | 13% helix, 22% strand | A0A2I8B6R1 |
| B | Brassinosteroid insensitive 1-associated receptor kinase 1 | protein | 176 | 22% helix, 14% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 31 copies · chains B, C, A
- BMA · beta-D-mannopyranose · sugar · 7 copies
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.75 | 0.89 | 41 | empty |
| 2 | 600 | 0.73 | 0.80 | 56 | empty |
| 3 | 50 | 0.65 | 0.95 | 18 | empty |
| 4 | 512 | 0.64 | 0.77 | 50 | MAN |
| 5 | 369 | 0.57 | 0.75 | 42 | NAG |
Interfaces
2 interfaces between chains.
- A–C · 2038 Ų buried · 16 hydrogen bonds · protein-protein
- C–B · 1096 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 7DRC · Cryo-EM structure of plant receptor like protein RXEG1 in complex with xyloglucanase XEG1… · 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 Q30BZ2
- Every structure of UniProt A0A2I8B6R1
- Elsewhere: RCSB PDB 7DRC · PDBe 7DRC · UniProt Q30BZ2 · UniProt A0A2I8B6R1
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