Research workbench
Structure of the apo form of a zingiber officinale double bond reductase
Analyse Structure of the apo form of a zingiber officinale double bond reductase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MKR
- Type
- protein
- Length
- 1,213 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zingiber officinale double bond reductase
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zingiber officinale double bond reductase | protein | 328 | 32% helix, 29% strand | — |
| B | Zingiber officinale double bond reductase | protein | 228 | 32% helix, 26% strand | — |
| C | Zingiber officinale double bond reductase | protein | 330 | 33% helix, 28% strand | — |
| D | Zingiber officinale double bond reductase | protein | 327 | 31% helix, 28% strand | — |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.74 | 0.80 | 61 | empty |
| 2 | 756 | 0.73 | 0.78 | 60 | empty |
| 3 | 692 | 0.72 | 0.78 | 62 | empty |
| 4 | 273 | 0.53 | 0.75 | 44 | empty |
| 5 | 56 | 0.34 | 0.77 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1084 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 980 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 77 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 60 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4MKR · Structure of the apo form of a Zingiber officinale double bond reductase · 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 4MKR · PDBe 4MKR
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