MolNFT v1 · #108666 · protein
Structure of the binary complex of a zingiber officinale double bond reductase in complex with NADP monoclinic crystal form
4WE3: “Structure of the binary complex of a zingiber officinale double bond reductase in complex with NADP…”. X-ray diffraction, 1 ligand (NAP), 13 pockets (best druggability 0.82). MolNFT v1 #108666 on GenesisL1: 3D structure, binding…
- PDB
- 4WE3
- Type
- protein
- Length
- 1,367 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Double bond reductase
- Ligands
- NAP
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Double bond reductase | protein | 342 | 31% helix, 27% strand | — |
| B | Double bond reductase | protein | 340 | 32% helix, 28% strand | — |
| C | Double bond reductase | protein | 343 | 31% helix, 27% strand | — |
| D | Double bond reductase | protein | 342 | 32% helix, 27% 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
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.82 | 0.89 | 55 | NAP |
| 2 | 881 | 0.80 | 0.82 | 82 | NAP |
| 3 | 580 | 0.79 | 0.85 | 73 | NAP |
| 4 | 872 | 0.76 | 0.79 | 64 | NAP |
| 5 | 812 | 0.72 | 0.78 | 56 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1179 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1130 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 402 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 165 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 4WE3 · Structure of the binary complex of a zingiber officinale double bond reductase in complex… · 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 4WE3 · PDBe 4WE3
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