Research workbench
Crystal structure of sulfolobus shibatae isopentenyl diphosphate isomerase in complex with oipp.
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
- 3B04
- Type
- protein
- Length
- 1,448 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
- OOP, MG
- Pockets
- 14 · best druggability 0.80
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 | 362 | 51% helix, 15% strand | P61615 |
Ligands and binding sites
- OOP · 1-deoxy-1-[(4aR)-4a-[(2R)-1-hydroxy-5-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-3-methylidenepentan-2-yl]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol · 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
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.80 | 0.90 | 50 | OOP, MG |
| 2 | 332 | 0.80 | 0.91 | 44 | OOP, MG |
| 3 | 327 | 0.80 | 0.91 | 46 | OOP, MG |
| 4 | 387 | 0.80 | 0.89 | 52 | OOP, MG |
| 5 | 372 | 0.58 | 0.76 | 51 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1591 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1588 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1575 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1572 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3B04 · 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 0.99
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 3B04 · PDBe 3B04 · UniProt P61615
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