MolNFT v1 · #140623 · protein
Crystal structure of plp bound diaminopropionate ammonia lyase from salmonella typhimurium
5YGR: “Crystal structure of plp bound diaminopropionate ammonia lyase from salmonella typhimurium”. X-ray diffraction, 1 ligand (PO4), 15 pockets (best druggability 0.80). MolNFT v1 #140623 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YGR
- Type
- protein
- Length
- 1,508 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopropionate ammonia lyase
- EC
- 4.3.1.15
- Ligands
- PO4
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopropionate ammonia lyase (EC 4.3.1.15) | protein | 375 | 48% helix, 15% strand | — |
| B | Diaminopropionate ammonia lyase (EC 4.3.1.15) | protein | 365 | 47% helix, 16% strand | — |
| C | Diaminopropionate ammonia lyase (EC 4.3.1.15) | protein | 380 | 47% helix, 15% strand | — |
| D | Diaminopropionate ammonia lyase (EC 4.3.1.15) | protein | 388 | 45% helix, 15% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 9 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.80 | 0.94 | 38 | empty |
| 2 | 155 | 0.72 | 0.91 | 28 | PO4 |
| 3 | 876 | 0.70 | 0.75 | 93 | empty |
| 4 | 158 | 0.68 | 0.89 | 31 | PO4 |
| 5 | 261 | 0.60 | 0.79 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1000 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 914 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 273 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 238 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 5YGR · Crystal structure of PLP bound Diaminopropionate ammonia lyase from Salmonella typhimurium · the same entry in another collection · chain D against D, 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
- Elsewhere: RCSB PDB 5YGR · PDBe 5YGR
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.