MolNFT v1 · #95906 · protein
Pyld in complex with L-lysine-ne-D-ornithine and NADH
4J4B: “Pyld in complex with L-lysine-ne-D-ornithine and NADH”. X-ray diffraction, 4 ligands (NAI, 0TF, NA), 5 pockets (best druggability 0.81). MolNFT v1 #95906 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4J4B
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyld
- EC
- 1.4.1.-
- UniProt
- Q46E80
- Ligands
- NAI, 0TF, NA, MG
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyld (EC 1.4.1.-) | protein | 259 | 40% helix, 20% strand | Q46E80 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- 0TF · N~6~-D-ornithyl-L-lysine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.81 | 0.84 | 101 | NAI, 0TF, MG |
| 2 | 437 | 0.79 | 0.87 | 47 | NAI, MG, 0TF |
| 3 | 151 | 0.41 | 0.74 | 23 | empty |
| 4 | 90 | 0.39 | 0.77 | 20 | empty |
| 5 | 98 | 0.39 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 471 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4J4B · PylD in complex with L-lysine-Ne-D-ornithine 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 4J4B · PDBe 4J4B · UniProt Q46E80
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