MolNFT v1 · #134737 · protein
Resurrected ancestral hydroxynitrile lyase from flowering plants
5TDX · Ancestral hydroxynitrile lyase 1: “Resurrected ancestral hydroxynitrile lyase from flowering plants”. X-ray diffraction, 14 pockets (best druggability 0.86). MolNFT v1 #134737 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5TDX
- Type
- protein
- Length
- 1,044 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ancestral hydroxynitrile lyase 1
- EC
- 4.1.2.47
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ancestral hydroxynitrile lyase 1 (EC 4.1.2.47) | protein | 260 | 41% helix, 18% strand | — |
| B | Ancestral hydroxynitrile lyase 1 (EC 4.1.2.47) | protein | 259 | 41% helix, 19% strand | — |
| C | Ancestral hydroxynitrile lyase 1 (EC 4.1.2.47) | protein | 265 | 41% helix, 19% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.86 | 0.87 | 99 | empty |
| 2 | 61 | 0.75 | 0.99 | 19 | GOL |
| 3 | 53 | 0.75 | 1.00 | 17 | GOL |
| 4 | 54 | 0.73 | 0.99 | 17 | GOL |
| 5 | 148 | 0.43 | 0.75 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 912 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 911 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 522 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 494 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 392 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5TDX · Resurrected Ancestral Hydroxynitrile Lyase from Flowering Plants · 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 5TDX · PDBe 5TDX
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