Research workbench
Crystal structure of an indole-3-acetic acid amido synthase from vitis vinifera involved in auxin homeostasis
Analyse Crystal structure of an indole-3-acetic acid amido synthase from vitis vinifera… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B2G
- Type
- protein
- Length
- 1,136 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GH3-1 auxin conjugating enzyme
- UniProt
- F6H697
- Ligands
- V1N
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GH3-1 auxin conjugating enzyme | protein | 564 | 39% helix, 22% strand | F6H697 |
| B | GH3-1 auxin conjugating enzyme | protein | 572 | 40% helix, 22% strand | F6H697 |
Ligands and binding sites
- V1N · [(2S,3R,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl] 2-(1H-indol-3-yl)ethyl hydrogen phosphate · ligand · 2 copies · chains A, B
- MLI · Malonate ion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.85 | 0.86 | 124 | MLI, V1N |
| 2 | 1127 | 0.85 | 0.85 | 116 | MLI, V1N |
| 3 | 183 | 0.57 | 0.81 | 24 | empty |
| 4 | 200 | 0.56 | 0.80 | 25 | empty |
| 5 | 159 | 0.43 | 0.74 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 638 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4B2G · Crystal Structure of an Indole-3-Acetic Acid Amido Synthase from Vitis vinifera Involved… · 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 F6H697
- Elsewhere: RCSB PDB 4B2G · PDBe 4B2G · UniProt F6H697
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