MolNFT v1 · #100523 · protein
Type 2 idi from S. pneumoniae
4N02 · Isopentenyl-diphosphate delta-isomerase: “Type 2 idi from S. pneumoniae”. X-ray diffraction, 2 ligands (FNR, SO4), 2 pockets (best druggability 0.80). MolNFT v1 #100523 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4N02
- Type
- protein
- Length
- 332 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isopentenyl-diphosphate delta-isomerase
- EC
- 5.3.3.2
- UniProt
- B2ILS5
- Ligands
- FNR, SO4
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2) | protein | 332 | 46% helix, 15% strand | B2ILS5 |
Ligands and binding sites
- FNR · 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydro-2H-benzo[g]pteridin-1-id-10(5H)-yl)-5-O-phosphonato-D-ribitol · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.80 | 0.88 | 57 | SO4, FNR |
| 2 | 176 | 0.51 | 0.77 | 22 | empty |
Compared structures
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 B2ILS5
- Elsewhere: RCSB PDB 4N02 · PDBe 4N02 · UniProt B2ILS5
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