MolNFT v1 · #95912 · protein
Pyld in complex with pyrroline-carboxy-lysine and NADH
4J4H: “Pyld in complex with pyrroline-carboxy-lysine and NADH”. X-ray diffraction, 4 ligands (NAI, 1J1, NA), 12 pockets (best druggability 0.83). MolNFT v1 #95912 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4J4H
- Type
- protein
- Length
- 1,036 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyld
- EC
- 1.4.1.-
- UniProt
- Q46E80
- Ligands
- NAI, 1J1, NA, MG
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyld (EC 1.4.1.-) | protein | 259 | 40% helix, 20% strand | Q46E80 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, C, B, D
- 1J1 · N~6~-[(2R)-3,4-dihydro-2H-pyrrol-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
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 | 950 | 0.83 | 0.84 | 98 | NAI, 1J1, MG |
| 2 | 434 | 0.78 | 0.87 | 47 | NAI, 1J1, MG |
| 3 | 494 | 0.77 | 0.85 | 53 | NAI, 1J1, MG |
| 4 | 453 | 0.76 | 0.84 | 50 | NAI, 1J1, MG |
| 5 | 523 | 0.66 | 0.77 | 45 | empty |
Interfaces
3 interfaces between chains.
- C–D · 961 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 488 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 394 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4J4H · PylD in complex with pyrroline-carboxy-lysine 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 4J4H · PDBe 4J4H · UniProt Q46E80
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