MolNFT v1 · #104195 · protein
Pyld in complex with pyrrolysine and NADH
4Q39 · Pyld, pyrrolysine synthase: “Pyld in complex with pyrrolysine and NADH”. X-ray diffraction, 4 ligands (NAI, PYL, NA), 4 pockets (best druggability 0.83). MolNFT v1 #104195 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4Q39
- Type
- protein
- Length
- 518 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
- NAI, PYL, NA, MG
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyld, pyrrolysine synthase (EC 1.4.1.-) | protein | 259 | 41% helix, 17% strand | Q46E80 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- PYL · Pyrrolysine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.83 | 0.86 | 95 | NAI, MG, PYL |
| 2 | 397 | 0.80 | 0.89 | 44 | NAI, MG, PYL |
| 3 | 174 | 0.43 | 0.74 | 23 | EDO |
| 4 | 96 | 0.38 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 459 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4Q39 · PylD in complex with pyrrolysine and NADH · 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 4Q39 · PDBe 4Q39 · UniProt Q46E80
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