Research workbench
Pyld cocrystallized with L-ornithine-nd-D-ornithine and NAD+
Analyse Pyld cocrystallized with L-ornithine-nd-D-ornithine and NAD+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q3D
- Type
- protein
- Length
- 1,020 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyld, pyrrolysine synthase
- EC
- 1.4.1.-
- UniProt
- Q46E80
- Ligands
- NAD, 2YH, NA, MG
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyld, pyrrolysine synthase (EC 1.4.1.-) | protein | 258 | 41% helix, 19% strand | Q46E80 |
| C | Pyld, pyrrolysine synthase (EC 1.4.1.-) | protein | 248 | 40% helix, 21% strand | Q46E80 |
| D | Pyld, pyrrolysine synthase (EC 1.4.1.-) | protein | 256 | 41% helix, 17% strand | Q46E80 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, C, B, D
- 2YH · N~5~-D-ornithyl-L-ornithine · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.73 | 0.83 | 45 | NAD, MG, 2YH |
| 2 | 423 | 0.73 | 0.83 | 46 | NAD, MG, 2YH |
| 3 | 51 | 0.71 | 0.98 | 14 | empty |
| 4 | 531 | 0.70 | 0.79 | 57 | NAD |
| 5 | 506 | 0.65 | 0.77 | 42 | empty |
Interfaces
3 interfaces between chains.
- C–D · 915 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 496 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 321 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4Q3D · PylD cocrystallized with L-Ornithine-Nd-D-ornithine 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 4Q3D · PDBe 4Q3D · UniProt Q46E80
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