MolNFT v1 · #54810 · protein
Structure of gcpe (ispg) from thermus thermophilus HB27
2Y0F · 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase: “Structure of gcpe (ispg) from thermus thermophilus HB27”. X-ray diffraction, 1 ligand (SF4), 18 pockets (best druggability 0.77). MolNFT v1 #54810 on GenesisL1: 3D structure…
- PDB
- 2Y0F
- Type
- protein
- Length
- 1,582 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
- EC
- 1.17.7.1
- UniProt
- Q72H18
- Ligands
- SF4
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (EC 1.17.7.1) | protein | 403 | 46% helix, 17% strand | Q72H18 |
| B | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (EC 1.17.7.1) | protein | 394 | 46% helix, 18% strand | Q72H18 |
| C | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (EC 1.17.7.1) | protein | 392 | 45% helix, 18% strand | Q72H18 |
| D | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (EC 1.17.7.1) | protein | 393 | 46% helix, 19% strand | Q72H18 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.77 | 0.79 | 70 | empty |
| 2 | 770 | 0.71 | 0.77 | 78 | empty |
| 3 | 585 | 0.66 | 0.76 | 62 | empty |
| 4 | 587 | 0.65 | 0.76 | 64 | empty |
| 5 | 598 | 0.65 | 0.75 | 64 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2039 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1994 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 756 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 103 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 97 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2Y0F · STRUCTURE OF GCPE (IspG) FROM THERMUS THERMOPHILUS HB27 · the same entry in another collection · chain D against D, TM-score 1.00
- Q72H18 · AlphaFold monomer V2.0 prediction for 4-hydroxy-3-methylbut-2-en-1-yl diphosphate… · a predicted model of the same protein · chain A against A, TM-score 0.73
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 Q72H18
- Elsewhere: RCSB PDB 2Y0F · PDBe 2Y0F · UniProt Q72H18
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