MolNFT v1 · #120722 · protein
Crystal structure of heptaprenyl diphosphate synthase from staphylococcus aureus
5H9D · Farnesyl pyrophosphate synthetase: “Crystal structure of heptaprenyl diphosphate synthase from staphylococcus aureus”. X-ray diffraction, 1 ligand (PO4), 10 pockets (best druggability 0.83). MolNFT v1 #120722 on GenesisL1: 3D…
- PDB
- 5H9D
- Type
- protein
- Length
- 1,046 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthetase; Heptaprenyl diphosphate synthase (heppp synthase)…
- EC
- 2.5.1.1, 2.5.1.30
- UniProt
- A0A0D6HKK2, W8TTD5
- Ligands
- PO4
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Farnesyl pyrophosphate synthetase (EC 2.5.1.1, 2.5.1.30) | protein | 318 | 73% helix, 1% strand | A0A0D6HKK2 |
| C, D | Heptaprenyl diphosphate synthase (heppp synthase) subunit 1 family protein | protein | 188 | 62% helix, 0% strand | W8TTD5 |
| K, L | C-terminal peptide from heptaprenyl diphosphate synthase (heppp synthase) subunit 1 family protein | protein | 17 | 71% helix, 0% strand | W8TTD5 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.83 | 0.86 | 70 | PO4 |
| 2 | 879 | 0.82 | 0.84 | 72 | PO4 |
| 3 | 656 | 0.76 | 0.81 | 59 | empty |
| 4 | 323 | 0.63 | 0.79 | 34 | empty |
| 5 | 341 | 0.61 | 0.78 | 31 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1967 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1952 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 533 Ų buried · 13 hydrogen bonds · protein-protein
- A–K · 486 Ų buried · 2 hydrogen bonds · protein-protein
- B–L · 483 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5H9D · Crystal structure of Heptaprenyl Diphosphate Synthase from Staphylococcus aureus · the same entry in another collection · chain C against C, 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 A0A0D6HKK2
- Every structure of UniProt W8TTD5
- Elsewhere: RCSB PDB 5H9D · PDBe 5H9D · UniProt A0A0D6HKK2 · UniProt W8TTD5
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