MolNFT v1 · #124250 · protein
Crystal structure of prib binary complex with product diphosphate
5K9M · Prib prenyltransferase: “Crystal structure of prib binary complex with product diphosphate”. X-ray diffraction, 1 ligand (POP), 2 pockets (best druggability 0.78). MolNFT v1 #124250 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5K9M
- Type
- protein
- Length
- 353 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prib prenyltransferase
- Ligands
- POP
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prib prenyltransferase | protein | 353 | 39% helix, 22% strand | — |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.78 | 0.92 | 37 | POP, TRS |
| 2 | 175 | 0.56 | 0.81 | 36 | empty |
Compared structures
- 5K9M · Crystal Structure of PriB Binary Complex with Product Diphosphate · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 5K9M · PDBe 5K9M
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