Research workbench
Crystal structure of arabidopsis thaliana ACO2 in complex with 2-pa
Analyse Crystal structure of arabidopsis thaliana ACO2 in complex with 2-pa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GJA
- Type
- protein
- Length
- 2,365 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-aminocyclopropane-1-carboxylate oxidase 2
- EC
- 1.14.17.4
- UniProt
- Q41931
- Ligands
- 6PC, ZN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 1-aminocyclopropane-1-carboxylate oxidase 2 (EC 1.14.17.4) | protein | 299 | 39% helix, 23% strand | Q41931 |
| B, C, F, G | 1-aminocyclopropane-1-carboxylate oxidase 2 (EC 1.14.17.4) | protein | 298 | 39% helix, 23% strand | Q41931 |
| E | 1-aminocyclopropane-1-carboxylate oxidase 2 (EC 1.14.17.4) | protein | 288 | 36% helix, 24% strand | Q41931 |
| H | 1-aminocyclopropane-1-carboxylate oxidase 2 (EC 1.14.17.4) | protein | 287 | 38% helix, 26% strand | Q41931 |
Ligands and binding sites
- 6PC · Pyridine-2-carboxylic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.80 | 0.82 | 97 | empty |
| 2 | 1121 | 0.78 | 0.80 | 81 | empty |
| 3 | 1140 | 0.72 | 0.76 | 97 | empty |
| 4 | 968 | 0.72 | 0.76 | 95 | empty |
| 5 | 632 | 0.69 | 0.77 | 57 | empty |
Interfaces
17 interfaces between chains.
- A–C · 926 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 906 Ų buried · 6 hydrogen bonds · protein-protein
- E–G · 406 Ų buried · 9 hydrogen bonds · protein-protein
- F–H · 390 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 372 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5GJA · Crystal structure of Arabidopsis thaliana ACO2 in complex with 2-PA · the same entry in another collection · chain H against H, TM-score 1.00
- Q41931 · AlphaFold monomer V2.0 prediction for 1-aminocyclopropane-1-carboxylate oxidase 2 (Q41931) · a predicted model of the same protein · chain D 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 Q41931
- Elsewhere: RCSB PDB 5GJA · PDBe 5GJA · UniProt Q41931
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