MolNFT v1 · #23414 · protein
Crystal structure of 1-aminocyclopropane-1-carboxylate-deaminase complexed with alpha-keto-butyrate
1TZK · 1-aminocyclopropane-1-carboxylate deaminase: “Crystal structure of 1-aminocyclopropane-1-carboxylate-deaminase complexed with alpha-keto-butyrate”. X-ray diffraction, 3 ligands (PLP, 2KT, SO4), 18 pockets (best druggability 0.77).…
- PDB
- 1TZK
- Type
- protein
- Length
- 1,324 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-aminocyclopropane-1-carboxylate deaminase
- EC
- 3.5.99.7
- UniProt
- Q00740
- Ligands
- PLP, 2KT, SO4
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7) | protein | 331 | 45% helix, 16% strand | Q00740 |
| B, D | 1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7) | protein | 329 | 46% helix, 16% strand | Q00740 |
| C | 1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7) | protein | 335 | 44% helix, 16% strand | Q00740 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- 2KT · 2-ketobutyric acid · ligand · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.77 | 0.98 | 37 | empty |
| 2 | 90 | 0.75 | 0.97 | 42 | empty |
| 3 | 185 | 0.65 | 0.85 | 38 | SO4, PLP |
| 4 | 300 | 0.62 | 0.80 | 47 | PLP, 2KT |
| 5 | 167 | 0.62 | 0.84 | 34 | PLP, 2KT |
Interfaces
6 interfaces between chains.
- C–D · 1782 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1781 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 610 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 564 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 196 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1TZK · Crystal structure of 1-aminocyclopropane-1-carboxylate-deaminase complexed with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q00740 · AlphaFold monomer V2.0 prediction for 1-aminocyclopropane-1-carboxylate deaminase (Q00740) · a predicted model of the same protein · chain B 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 Q00740
- Elsewhere: RCSB PDB 1TZK · PDBe 1TZK · UniProt Q00740
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