MolNFT v1 · #79026 · protein
Crystal structure of S. mutans isopentenyl pyrophosphate isomerase
3SR7 · Isopentenyl-diphosphate delta-isomerase: “Crystal structure of S. mutans isopentenyl pyrophosphate isomerase”. X-ray diffraction, 1 ligand (PO4), 13 pockets (best druggability 0.59). MolNFT v1 #79026 on GenesisL1: 3D structure…
- PDB
- 3SR7
- Type
- protein
- Length
- 1,078 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
- Q8DUI9
- Ligands
- PO4
- Pockets
- 13 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2) | protein | 273 | 46% helix, 17% strand | Q8DUI9 |
| B | Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2) | protein | 262 | 47% helix, 18% strand | Q8DUI9 |
| C | Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2) | protein | 272 | 45% helix, 17% strand | Q8DUI9 |
| D | Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2) | protein | 271 | 45% helix, 18% strand | Q8DUI9 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.59 | 0.80 | 29 | empty |
| 2 | 181 | 0.59 | 0.81 | 29 | empty |
| 3 | 161 | 0.51 | 0.79 | 29 | empty |
| 4 | 123 | 0.51 | 0.81 | 19 | empty |
| 5 | 133 | 0.48 | 0.79 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1651 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1530 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1409 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1194 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 32 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3SR7 · Crystal structure of S. mutans isopentenyl pyrophosphate isomerase · the same entry in another collection · chain D against D, TM-score 1.00
- Q8DUI9 · AlphaFold monomer V2.0 prediction for isopentenyl-diphosphate delta- isomerase (Q8DUI9) · a predicted model of the same protein · chain D 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 Q8DUI9
- Elsewhere: RCSB PDB 3SR7 · PDBe 3SR7 · UniProt Q8DUI9
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