MolNFT v1 · #95904 · protein
Pyld holoenzyme soaked with L-lysine-ne-D-ornithine
4J49: “Pyld holoenzyme soaked with L-lysine-ne-D-ornithine”. X-ray diffraction, 5 ligands (NAD, NAI, 1J1), 5 pockets (best druggability 0.69). MolNFT v1 #95904 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4J49
- Type
- protein
- Length
- 506 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyld
- EC
- 1.4.1.-
- UniProt
- Q46E80
- Ligands
- NAD, NAI, 1J1, NA, MG
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyld (EC 1.4.1.-) | protein | 250 | 42% helix, 20% strand | Q46E80 |
| B | Pyld (EC 1.4.1.-) | protein | 256 | 41% helix, 20% strand | Q46E80 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains B
- 1J1 · N~6~-[(2R)-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]-L-lysine · ligand · chains 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 | 425 | 0.69 | 0.81 | 43 | NAI, 1J1, MG |
| 2 | 348 | 0.60 | 0.77 | 43 | empty |
| 3 | 139 | 0.46 | 0.77 | 27 | empty |
| 4 | 165 | 0.46 | 0.76 | 27 | NAD, MG |
| 5 | 63 | 0.31 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 520 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4J49 · PylD holoenzyme soaked with L-lysine-Ne-D-ornithine · 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 4J49 · PDBe 4J49 · UniProt Q46E80
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