MolNFT v1 · #124502 · protein
Crystal structure of steptococcus pneumoniae undecaprenyl pyrophosphate synthase (upps) with farnesyl diphosphate
5KH4 · Isoprenyl transferase: “Crystal structure of steptococcus pneumoniae undecaprenyl pyrophosphate synthase (upps) with farnesyl…”. X-ray diffraction, 1 ligand (FPP), 3 pockets (best druggability 0.76). MolNFT v1 #124502 on GenesisL1…
- PDB
- 5KH4
- Type
- protein
- Length
- 461 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoprenyl transferase
- EC
- 2.5.1.-
- UniProt
- Q97SR4
- Ligands
- FPP
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoprenyl transferase (EC 2.5.1.-) | protein | 231 | 53% helix, 15% strand | Q97SR4 |
| B | Isoprenyl transferase (EC 2.5.1.-) | protein | 230 | 52% helix, 15% strand | Q97SR4 |
Ligands and binding sites
- FPP · Farnesyl diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.76 | 0.88 | 43 | FPP |
| 2 | 278 | 0.76 | 0.88 | 45 | FPP |
| 3 | 71 | 0.75 | 0.99 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1712 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5KH4 · Crystal Structure of Steptococcus pneumoniae Undecaprenyl pyrophosphate Synthase (UPPS)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q97SR4 · AlphaFold monomer V2.0 prediction for isoprenyl transferase (Q97SR4) · a predicted model of the same protein · chain B 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 Q97SR4
- Elsewhere: RCSB PDB 5KH4 · PDBe 5KH4 · UniProt Q97SR4
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