MolNFT v1 · #83905 · protein
S-selective hydroxynitrile lyase from baliospermum montanum (APO2)
3WWP · (S)-hydroxynitrile lyase: “S-selective hydroxynitrile lyase from baliospermum montanum (APO2)”. X-ray diffraction, 2 ligands (SO4, CL), 20 pockets (best druggability 0.75). MolNFT v1 #83905 on GenesisL1: 3D structure, binding sites…
- PDB
- 3WWP
- Type
- protein
- Length
- 1,568 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (S)-hydroxynitrile lyase
- UniProt
- D1MX73
- Ligands
- SO4, CL
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (S)-hydroxynitrile lyase | protein | 265 | 40% helix, 20% strand | D1MX73 |
| B | (S)-hydroxynitrile lyase | protein | 261 | 39% helix, 19% strand | D1MX73 |
| G | (S)-hydroxynitrile lyase | protein | 262 | 39% helix, 19% strand | D1MX73 |
| L | (S)-hydroxynitrile lyase | protein | 257 | 39% helix, 19% strand | D1MX73 |
| M | (S)-hydroxynitrile lyase | protein | 258 | 39% helix, 19% strand | D1MX73 |
| R | (S)-hydroxynitrile lyase | protein | 265 | 37% helix, 20% strand | D1MX73 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 18 copies · chains A, B, L, G, R
- CL · Chloride ion · ion · 6 copies · chains A, B, G, L, M, R
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B, G, L, M, R
- CIT · Citric acid · additive · 6 copies · chains A, B, G, L, M, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.75 | 0.78 | 64 | SO4 |
| 2 | 339 | 0.68 | 0.81 | 52 | EDO, CL |
| 3 | 150 | 0.67 | 0.87 | 35 | EDO, CL |
| 4 | 144 | 0.67 | 0.88 | 34 | EDO, CL |
| 5 | 135 | 0.66 | 0.88 | 33 | EDO, CL |
Interfaces
8 interfaces between chains.
- A–R · 1039 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 947 Ų buried · 0 hydrogen bonds · protein-protein
- M–R · 933 Ų buried · 2 hydrogen bonds · protein-protein
- G–L · 925 Ų buried · 1 hydrogen bond · protein-protein
- B–L · 464 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3WWP · S-selective hydroxynitrile lyase from Baliospermum montanum (apo2) · 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
- Every structure of UniProt D1MX73
- Elsewhere: RCSB PDB 3WWP · PDBe 3WWP · UniProt D1MX73
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