Research workbench
Crystal structure analysis of the acc deaminase homologue
Analyse Crystal structure analysis of the acc deaminase homologue in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J0A
- Type
- protein
- Length
- 975 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-aminocyclopropane-1-carboxylate deaminase
- EC
- 4.1.99.4
- UniProt
- O57809
- Ligands
- PLP, SO4
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 1-aminocyclopropane-1-carboxylate deaminase (EC 4.1.99.4) | protein | 325 | 45% helix, 16% strand | O57809 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- IPA · Isopropyl alcohol · additive · chains A
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 | 141 | 0.81 | 0.98 | 28 | empty |
| 2 | 709 | 0.77 | 0.82 | 88 | SO4, PLP |
| 3 | 264 | 0.76 | 0.89 | 63 | SO4, PLP |
| 4 | 395 | 0.71 | 0.83 | 59 | SO4, PLP |
| 5 | 704 | 0.69 | 0.76 | 47 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1712 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 353 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 67 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1J0A · Crystal Structure Analysis of the ACC deaminase homologue · the same entry in another collection · chain A against A, TM-score 1.00
- O57809 · AlphaFold monomer V2.0 prediction for putative 1-aminocyclopropane-1-carboxylate… · 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 O57809
- Elsewhere: RCSB PDB 1J0A · PDBe 1J0A · UniProt O57809
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