Research workbench
Crystal structure of diaminopropionate ammonia lyase from escherichia COLI in complex with aminoacrylate-plp azomethine reaction intermediate
Analyse Crystal structure of diaminopropionate ammonia lyase from escherichia COLI in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D9M
- Type
- protein
- Length
- 761 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopropionate ammonia-lyase
- EC
- 4.3.1.15
- UniProt
- P66899
- Ligands
- 0JO
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopropionate ammonia-lyase (EC 4.3.1.15) | protein | 378 | 44% helix, 15% strand | P66899 |
| B | Diaminopropionate ammonia-lyase (EC 4.3.1.15) | protein | 383 | 45% helix, 15% strand | P66899 |
Ligands and binding sites
- 0JO · 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.77 | 0.96 | 26 | 0JO |
| 2 | 291 | 0.74 | 0.87 | 47 | 0JO |
| 3 | 128 | 0.60 | 0.85 | 21 | empty |
| 4 | 150 | 0.54 | 0.80 | 22 | empty |
| 5 | 113 | 0.38 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1101 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4D9M · Crystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex… · the same entry in another collection · chain B against B, TM-score 1.00
- P66899 · AlphaFold monomer V2.0 prediction for diaminopropionate ammonia-lyase (P66899) · a predicted model of the same protein · chain A 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 P66899
- Elsewhere: RCSB PDB 4D9M · PDBe 4D9M · UniProt P66899
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