MolNFT v1 · #104197 · protein
Pyld cocrystallized with L-lysine-ne-D-lysine and NAD+
4Q3B · Pyld, pyrrolysine synthase: “Pyld cocrystallized with L-lysine-ne-D-lysine and NAD+”. X-ray diffraction, 4 ligands (NAI, 2YF, NA), 12 pockets (best druggability 0.82). MolNFT v1 #104197 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4Q3B
- Type
- protein
- Length
- 1,040 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
- NAI, 2YF, NA, MG
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyld, pyrrolysine synthase (EC 1.4.1.-) | protein | 260 | 40% helix, 17% strand | Q46E80 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, D, B, C
- 2YF · N~6~-[(2R)-2,3,4,5-tetrahydropyridin-2-ylcarbonyl]-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 · 15 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C
- 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
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.82 | 0.84 | 101 | NAI, MG, 2YF |
| 2 | 462 | 0.79 | 0.87 | 51 | NAI, MG, 2YF |
| 3 | 426 | 0.78 | 0.87 | 49 | NAI, MG, 2YF, EDO |
| 4 | 447 | 0.78 | 0.86 | 48 | NAI, MG, 2YF |
| 5 | 437 | 0.70 | 0.81 | 53 | empty |
Interfaces
3 interfaces between chains.
- A–D · 591 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 584 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 498 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4Q3B · PylD cocrystallized with L-Lysine-Ne-D-lysine and NAD+ · the same entry in another collection · chain B against B, 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 4Q3B · PDBe 4Q3B · UniProt Q46E80
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.