MolNFT v1 · #58328 · protein
Crystal structure of sulfolobus shibatae isopentenyl diphosphate isomerase in complex with vipp.
3B03 · Isopentenyl-diphosphate delta-isomerase: “Crystal structure of sulfolobus shibatae isopentenyl diphosphate isomerase in complex with vipp.”. X-ray diffraction, 2 ligands (VNR, MG), 11 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 3B03
- Type
- protein
- Length
- 1,455 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
- VNR, MG
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2) | protein | 363 | 51% helix, 15% strand | P61615 |
| B, C, D | Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2) | protein | 364 | 51% helix, 15% strand | P61615 |
Ligands and binding sites
- VNR · 1-deoxy-1-[(4aR)-4a-[(2Z)-2-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)but-2-en-1-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 · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.83 | 0.94 | 47 | MG, VNR |
| 2 | 289 | 0.82 | 0.93 | 48 | VNR |
| 3 | 293 | 0.81 | 0.93 | 49 | VNR, MG |
| 4 | 291 | 0.81 | 0.93 | 50 | MG, VNR |
| 5 | 673 | 0.69 | 0.77 | 93 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1582 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1581 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1574 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1572 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3B03 · 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 3B03 · PDBe 3B03 · UniProt P61615
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