Research workbench
Pyld cocrystallized with L-lysine-ne-L-lysine and NAD+
Analyse Pyld cocrystallized with L-lysine-ne-L-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
- 4Q3C
- Type
- protein
- Length
- 1,035 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, 2YG, NA, MG
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Pyld, pyrrolysine synthase (EC 1.4.1.-) | protein | 259 | 40% helix, 20% strand | Q46E80 |
| D | Pyld, pyrrolysine synthase (EC 1.4.1.-) | protein | 258 | 41% helix, 20% strand | Q46E80 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C
- 2YG · N~6~-L-lysyl-L-lysine · 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
- GOL · Glycerol · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.79 | 0.88 | 44 | NAD, MG, 2YG |
| 2 | 399 | 0.78 | 0.87 | 45 | NAD, MG, 2YG |
| 3 | 427 | 0.76 | 0.85 | 48 | NAD, MG, 2YG |
| 4 | 442 | 0.76 | 0.85 | 44 | NAD, MG, 2YG |
| 5 | 306 | 0.70 | 0.83 | 44 | NAD |
Interfaces
3 interfaces between chains.
- A–B · 511 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 426 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 415 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4Q3C · PylD cocrystallized with L-Lysine-Ne-L-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 4Q3C · PDBe 4Q3C · UniProt Q46E80
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