Research workbench
Pyld cocrystallized with L-ornithine-nd-D-lysine and NAD+
Analyse Pyld cocrystallized with L-ornithine-nd-D-lysine and NAD+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q3E
- Type
- protein
- Length
- 508 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyld, pyrrolysine synthase
- EC
- 1.4.1.-
- UniProt
- Q46E80
- Ligands
- NAD, 2YJ, NA, MG, SO4
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyld, pyrrolysine synthase (EC 1.4.1.-) | protein | 253 | 42% helix, 20% strand | Q46E80 |
| B | Pyld, pyrrolysine synthase (EC 1.4.1.-) | protein | 255 | 42% helix, 20% strand | Q46E80 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- 2YJ · N~5~-D-lysyl-L-ornithine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.65 | 0.79 | 38 | empty |
| 2 | 313 | 0.58 | 0.77 | 37 | NAD, MG, 2YJ |
| 3 | 234 | 0.51 | 0.75 | 43 | NAD, MG, 2YJ |
| 4 | 95 | 0.36 | 0.75 | 21 | EDO |
Interfaces
1 interface between chains.
- A–B · 565 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4Q3E · PylD cocrystallized with L-Ornithine-Nd-D-lysine and NAD+ · the same entry in another collection · 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 Q46E80
- Elsewhere: RCSB PDB 4Q3E · PDBe 4Q3E · UniProt Q46E80
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