MolNFT v1 · #140981 · protein
Ethanolamine ammonia-lyase, ADOCBL/SUBSTRATE-free
5YSN · Ethanolamine ammonia-lyase heavy chain: “Ethanolamine ammonia-lyase, ADOCBL/SUBSTRATE-free”. X-ray diffraction, 2 ligands (5AD, B12), 16 pockets (best druggability 0.85). MolNFT v1 #140981 on GenesisL1: 3D structure, binding sites…
- PDB
- 5YSN
- Type
- protein
- Length
- 1,410 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ethanolamine ammonia-lyase heavy chain; Ethanolamine ammonia-lyase light chain
- EC
- 4.3.1.7
- UniProt
- P0AEJ6, P19636
- Ligands
- 5AD, B12
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ethanolamine ammonia-lyase heavy chain (EC 4.3.1.7) | protein | 453 | 48% helix, 14% strand | P0AEJ6 |
| B, D | Ethanolamine ammonia-lyase light chain (EC 4.3.1.7) | protein | 252 | 45% helix, 17% strand | P19636 |
Ligands and binding sites
- 5AD · 5'-deoxyadenosine · ligand · 2 copies · chains A, C
- B12 · Cobalamin · ligand · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 11 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.85 | 0.85 | 63 | 5AD, B12 |
| 2 | 1015 | 0.84 | 0.85 | 67 | 5AD, B12 |
| 3 | 364 | 0.73 | 0.84 | 48 | GOL |
| 4 | 349 | 0.72 | 0.84 | 57 | empty |
| 5 | 138 | 0.57 | 0.83 | 28 | GOL |
Interfaces
5 interfaces between chains.
- A–B · 2261 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2214 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 1391 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 977 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 970 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5YSN · Ethanolamine ammonia-lyase, AdoCbl/substrate-free · the same entry in another collection · chain D against D, TM-score 1.00
- P0AEJ6 · AlphaFold monomer V2.0 prediction for ethanolamine ammonia-lyase heavy chain (P0AEJ6) · a predicted model of the same protein · chain C against A, TM-score 1.00
- P19636 · AlphaFold monomer V2.0 prediction for ethanolamine ammonia-lyase light chain (P19636) · 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 P0AEJ6
- Every structure of UniProt P19636
- Elsewhere: RCSB PDB 5YSN · PDBe 5YSN · UniProt P0AEJ6 · UniProt P19636
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