MolNFT v1 · #29926 · protein
Structure of the synthase subunit of plp synthase
1ZNN: “Structure of the synthase subunit of plp synthase”. X-ray diffraction, 1 ligand (SO4), 13 pockets (best druggability 0.63). MolNFT v1 #29926 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1ZNN
- Type
- protein
- Length
- 1,470 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plp synthase
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Plp synthase | protein | 245 | 47% helix, 16% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, F
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.63 | 0.80 | 43 | SO4, MRD |
| 2 | 248 | 0.61 | 0.80 | 38 | SO4, MRD |
| 3 | 219 | 0.60 | 0.81 | 35 | SO4, MRD |
| 4 | 206 | 0.60 | 0.81 | 38 | SO4, MRD |
| 5 | 208 | 0.59 | 0.80 | 38 | SO4, MRD |
Interfaces
6 interfaces between chains.
- E–F · 1003 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 999 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 994 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 974 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 973 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1ZNN · Structure of the synthase subunit of PLP synthase · 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 1ZNN · PDBe 1ZNN
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