Research workbench
Crystal structure of sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced FMN and ipp.
Analyse Crystal structure of sulfolobus shibatae isopentenyl diphosphate isomerase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZRY
- Type
- protein
- Length
- 1,456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isopentenyl-diphosphate delta-isomerase
- EC
- 5.3.3.2
- UniProt
- P61615
- Ligands
- FNR, IPE, MG
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2) | protein | 364 | 51% helix, 15% strand | P61615 |
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 · 4 copies · chains A, B, C, D
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.83 | 0.95 | 45 | FNR, IPE, MG |
| 2 | 252 | 0.83 | 0.95 | 46 | FNR, IPE, MG |
| 3 | 249 | 0.83 | 0.95 | 45 | FNR, IPE, MG |
| 4 | 251 | 0.82 | 0.94 | 45 | FNR, IPE, MG |
| 5 | 185 | 0.52 | 0.78 | 29 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1549 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1547 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1538 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1538 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2ZRY · Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P61615 · AlphaFold monomer V2.0 prediction for isopentenyl-diphosphate delta- isomerase (P61615) · a predicted model of the same protein · 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 P61615
- Elsewhere: RCSB PDB 2ZRY · PDBe 2ZRY · UniProt P61615
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