Research workbench
11S globulin from wrightia tinctoria reveals auxin binding site
Analyse 11S globulin from wrightia tinctoria reveals auxin binding site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WXU
- Type
- protein
- Length
- 2,387 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 11S globulin
- UniProt
- A0A162EGL7
- Ligands
- IAC, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 11S globulin | protein | 399 | 15% helix, 38% strand | A0A162EGL7 |
| B | 11S globulin | protein | 400 | 15% helix, 39% strand | A0A162EGL7 |
| C, E | 11S globulin | protein | 397 | 14% helix, 39% strand | A0A162EGL7 |
| D | 11S globulin | protein | 396 | 14% helix, 39% strand | A0A162EGL7 |
| F | 11S globulin | protein | 398 | 14% helix, 39% strand | A0A162EGL7 |
Ligands and binding sites
- IAC · 1H-indol-3-ylacetic acid · ligand · 3 copies · chains A, C, E, F, B, D
- PO4 · Phosphate ion · ion · 18 copies · chains A, B, F, C, D, E
- GOL · Glycerol · additive · 9 copies · chains A, B, C, E, F
- FLC · Citrate anion · additive · 6 copies · chains A, F, B, D, C, E
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, D, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.85 | 0.86 | 102 | PO4 |
| 2 | 1137 | 0.84 | 0.85 | 108 | PO4 |
| 3 | 567 | 0.79 | 0.86 | 66 | FLC, GOL |
| 4 | 597 | 0.78 | 0.84 | 51 | GOL, FLC |
| 5 | 513 | 0.75 | 0.84 | 40 | FLC, GOL |
Interfaces
14 interfaces between chains.
- A–B · 3127 Ų buried · 70 hydrogen bonds · protein-protein
- B–C · 3124 Ų buried · 60 hydrogen bonds · protein-protein
- E–F · 3110 Ų buried · 61 hydrogen bonds · protein-protein
- A–C · 3087 Ų buried · 63 hydrogen bonds · protein-protein
- D–F · 3082 Ų buried · 61 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5WXU · 11S globulin from Wrightia tinctoria reveals auxin binding site · 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 A0A162EGL7
- Elsewhere: RCSB PDB 5WXU · PDBe 5WXU · UniProt A0A162EGL7
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