MolNFT v1 · #77416 · protein
3.0 a structure of the prunus mume hydroxynitrile lyase isozyme-1
3RED: “3.0 a structure of the prunus mume hydroxynitrile lyase isozyme-1”. X-ray diffraction, 1 ligand (FAD), 20 pockets (best druggability 0.88). MolNFT v1 #77416 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3RED
- Type
- protein
- Length
- 6,252 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxynitrile lyase
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Hydroxynitrile lyase | protein | 521 | 27% helix, 26% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.88 | 0.90 | 141 | FAD |
| 2 | 511 | 0.88 | 0.94 | 76 | FAD |
| 3 | 559 | 0.88 | 0.93 | 77 | FAD |
| 4 | 527 | 0.88 | 0.94 | 73 | FAD |
| 5 | 425 | 0.87 | 0.95 | 58 | FAD |
Interfaces
27 interfaces between chains.
- D–E · 737 Ų buried · 4 hydrogen bonds · protein-protein
- F–G · 729 Ų buried · 5 hydrogen bonds · protein-protein
- I–J · 716 Ų buried · 7 hydrogen bonds · protein-protein
- A–H · 708 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 692 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3RED · 3.0 A structure of the Prunus mume hydroxynitrile lyase isozyme-1 · 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 3RED · PDBe 3RED
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