Research workbench
Crystal structure of acc deaminase complexed with substrate analog B- chloro-D-alanine
Analyse Crystal structure of acc deaminase complexed with substrate analog B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TZM
- 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, C2N, NAK, SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7) | protein | 331 | 43% helix, 15% strand | Q00740 |
| B | 1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7) | protein | 328 | 44% helix, 16% strand | Q00740 |
| C | 1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7) | protein | 338 | 43% 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
- C2N · 3-chloro-D-alanine · ligand · 2 copies · chains A, C
- NAK · Amino-acrylate · 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
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.76 | 0.98 | 39 | empty |
| 2 | 71 | 0.73 | 0.98 | 30 | empty |
| 3 | 67 | 0.71 | 0.97 | 29 | SO4, PLP |
| 4 | 323 | 0.65 | 0.80 | 41 | PLP, C2N, NAK |
| 5 | 189 | 0.59 | 0.82 | 36 | SO4, PLP |
Interfaces
6 interfaces between chains.
- C–D · 1794 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1784 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 600 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 559 Ų buried · 6 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
- 1TZM · Crystal structure of ACC deaminase complexed with substrate analog b-chloro-D-alanine · 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 1TZM · PDBe 1TZM · UniProt Q00740
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