Research workbench
Crystal structure of apple acc synthase in complex with L-vinylglycine
Analyse Crystal structure of apple acc synthase in complex with L-vinylglycine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YNU
- Type
- protein
- Length
- 417 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-aminocyclopropane-1-carboxylate synthase
- EC
- 4.4.1.14
- UniProt
- P37821
- Ligands
- PY4, NI, K
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-aminocyclopropane-1-carboxylate synthase (EC 4.4.1.14) | protein | 417 | 46% helix, 16% strand | P37821 |
Ligands and binding sites
- PY4 · 2-[O-phosphonopyridoxyl]-amino- butyric acid · ligand · chains A
- NI · Nickel (II) ion · metal · 2 copies · chains A
- K · Potassium ion · metal · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.62 | 0.85 | 25 | PY4 |
| 2 | 94 | 0.60 | 0.87 | 31 | empty |
| 3 | 57 | 0.29 | 0.75 | 14 | empty |
| 4 | 52 | 0.27 | 0.74 | 12 | empty |
| 5 | 60 | 0.26 | 0.72 | 17 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1YNU · Crystal structure of apple ACC synthase in complex with L-vinylglycine · the same entry in another collection · chain A against A, TM-score 1.00
- P37821 · AlphaFold monomer V2.0 prediction for 1-aminocyclopropane-1-carboxylate synthase (P37821) · a predicted model of the same protein · chain A 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 P37821
- Elsewhere: RCSB PDB 1YNU · PDBe 1YNU · UniProt P37821
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