MolNFT v1 · #157826 · protein
Crystal structure of piper methysticum kavalactone reductase 1 in complex with NADP
6NBR: “Crystal structure of piper methysticum kavalactone reductase 1 in complex with NADP”. X-ray diffraction, 1 ligand (NAP), 9 pockets (best druggability 0.84). MolNFT v1 #157826 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6NBR
- Type
- protein
- Length
- 1,260 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kavalactone reductase 1
- Ligands
- NAP
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Kavalactone reductase 1 | protein | 316 | 41% helix, 16% strand | — |
| C, D | Kavalactone reductase 1 | protein | 314 | 42% helix, 16% strand | — |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.84 | 0.85 | 103 | NAP |
| 2 | 705 | 0.81 | 0.85 | 75 | NAP |
| 3 | 1040 | 0.79 | 0.80 | 86 | NAP |
| 4 | 1003 | 0.79 | 0.80 | 83 | NAP |
| 5 | 224 | 0.56 | 0.79 | 37 | empty |
Interfaces
5 interfaces between chains.
- C–D · 472 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 417 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 357 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 183 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 168 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6NBR · Crystal Structure of Piper methysticum Kavalactone Reductase 1 in complex with NADP · 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
- Elsewhere: RCSB PDB 6NBR · PDBe 6NBR
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