MolNFT v1 · #23413 · protein
Crystal structure of 1-aminocyclopropane-1-carboxylate deaminase complexed with D-vinyl glycine
1TZJ: “Crystal structure of 1-aminocyclopropane-1-carboxylate deaminase complexed with D-vinyl glycine”. X-ray diffraction, 3 ligands (PLP, A3B, SO4), 19 pockets (best druggability 0.75). MolNFT v1 #23413 on GenesisL1: 3D structure…
- PDB
- 1TZJ
- Type
- protein
- Length
- 1,326 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, A3B, SO4
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 4 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 | 1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7) | protein | 328 | 45% helix, 16% strand | Q00740 |
| C | 1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7) | protein | 338 | 45% helix, 15% strand | Q00740 |
| D | 1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7) | protein | 329 | 44% helix, 16% strand | Q00740 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- A3B · D-vinylglycine · 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
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.75 | 0.98 | 34 | empty |
| 2 | 59 | 0.69 | 0.97 | 24 | empty |
| 3 | 198 | 0.66 | 0.85 | 40 | SO4, PLP |
| 4 | 190 | 0.64 | 0.84 | 36 | SO4, PLP |
| 5 | 314 | 0.64 | 0.80 | 42 | PLP, A3B |
Interfaces
6 interfaces between chains.
- C–D · 1792 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1772 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 597 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 569 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 196 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1TZJ · Crystal Structure of 1-aminocyclopropane-1-carboxylate deaminase complexed with d-vinyl… · 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 1TZJ · PDBe 1TZJ · UniProt Q00740
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