Research workbench
Crystal structure analysis of the acc deaminase homologue complexed with inhibitor
Analyse Crystal structure analysis of the acc deaminase homologue complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J0B
- Type
- protein
- Length
- 7,800 residues
- Chains
- 24
- 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
- 5PA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X | 1-aminocyclopropane-1-carboxylate deaminase (EC 4.1.99.4) | protein | 325 | 45% helix, 16% strand | O57809 |
Ligands and binding sites
- 5PA · N-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-Y-lmethyl]-1-amino-cyclopropanecarboxylic acid · ligand · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.82 | 0.83 | 121 | empty |
| 2 | 145 | 0.82 | 0.98 | 31 | empty |
| 3 | 149 | 0.81 | 0.98 | 34 | empty |
| 4 | 725 | 0.81 | 0.85 | 91 | empty |
| 5 | 131 | 0.81 | 0.98 | 31 | empty |
Interfaces
42 interfaces between chains.
- O–P · 1737 Ų buried · 12 hydrogen bonds · protein-protein
- I–J · 1732 Ų buried · 14 hydrogen bonds · protein-protein
- Q–R · 1724 Ų buried · 17 hydrogen bonds · protein-protein
- S–T · 1717 Ų buried · 16 hydrogen bonds · protein-protein
- W–X · 1717 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1J0B · Crystal Structure Analysis of the ACC deaminase homologue complexed with inhibitor · the same entry in another collection · chain K against K, 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 O57809
- Elsewhere: RCSB PDB 1J0B · PDBe 1J0B · UniProt O57809
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