Research workbench
Crystal structure of GH3.5 acyl acid amido synthetase from arabidopsis thaliana
Analyse Crystal structure of GH3.5 acyl acid amido synthetase from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KOD
- Type
- protein
- Length
- 2,278 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Indole-3-acetic acid-amido synthetase GH3.5
- EC
- 6.3.2.-
- UniProt
- O81829
- Ligands
- AMP, IAC, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indole-3-acetic acid-amido synthetase GH3.5 (EC 6.3.2.-) | protein | 573 | 41% helix, 22% strand | O81829 |
| B | Indole-3-acetic acid-amido synthetase GH3.5 (EC 6.3.2.-) | protein | 573 | 41% helix, 22% strand | O81829 |
| C | Indole-3-acetic acid-amido synthetase GH3.5 (EC 6.3.2.-) | protein | 566 | 42% helix, 22% strand | O81829 |
| D | Indole-3-acetic acid-amido synthetase GH3.5 (EC 6.3.2.-) | protein | 566 | 42% helix, 21% strand | O81829 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- IAC · 1H-indol-3-ylacetic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.88 | 0.91 | 93 | AMP, IAC, SO4 |
| 2 | 1091 | 0.88 | 0.89 | 119 | AMP, IAC |
| 3 | 1022 | 0.86 | 0.87 | 106 | AMP, IAC |
| 4 | 1132 | 0.85 | 0.86 | 119 | AMP, IAC |
| 5 | 1112 | 0.78 | 0.80 | 97 | empty |
Interfaces
4 interfaces between chains.
- A–B · 489 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 438 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 323 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 179 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 5KOD · Crystal Structure of GH3.5 Acyl Acid Amido Synthetase from Arabidopsis thaliana · the same entry in another collection · chain C against C, TM-score 1.00
- O81829 · AlphaFold monomer V2.0 prediction for indole-3-acetic acid-amido synthetase GH3.5 (O81829) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 O81829
- Elsewhere: RCSB PDB 5KOD · PDBe 5KOD · UniProt O81829
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