MolNFT v1 · #124500 · protein
Crystal structure of steptococcus pneumoniae undecaprenyl pyrophosphate synthase (upps)
5KH2 · Isoprenyl transferase: “Crystal structure of steptococcus pneumoniae undecaprenyl pyrophosphate synthase (upps)”. X-ray diffraction, 9 pockets (best druggability 0.76). MolNFT v1 #124500 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5KH2
- Type
- protein
- Length
- 886 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoprenyl transferase
- EC
- 2.5.1.-
- UniProt
- Q97SR4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoprenyl transferase (EC 2.5.1.-) | protein | 224 | 51% helix, 13% strand | Q97SR4 |
| B | Isoprenyl transferase (EC 2.5.1.-) | protein | 223 | 53% helix, 14% strand | Q97SR4 |
| C | Isoprenyl transferase (EC 2.5.1.-) | protein | 222 | 52% helix, 14% strand | Q97SR4 |
| D | Isoprenyl transferase (EC 2.5.1.-) | protein | 217 | 51% helix, 14% strand | Q97SR4 |
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.76 | 0.79 | 91 | empty |
| 2 | 60 | 0.73 | 0.99 | 24 | empty |
| 3 | 293 | 0.69 | 0.83 | 31 | empty |
| 4 | 575 | 0.69 | 0.78 | 58 | empty |
| 5 | 205 | 0.68 | 0.85 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1741 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1683 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 253 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 250 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 43 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5KH2 · Crystal Structure of Steptococcus pneumoniae Undecaprenyl pyrophosphate Synthase (UPPS) · the same entry in another collection · chain D against D, 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 5KH2 · PDBe 5KH2 · UniProt Q97SR4
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