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Crystal structure of limf prenyltransferase bound with a peptide substrate and gspp
Analyse Crystal structure of limf prenyltransferase bound with a peptide substrate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VMW
- Type
- protein
- Length
- 595 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LYNF/TRUF/PATF family peptide O-prenyltransferase; Substrate peptide
- UniProt
- A0A372DCN7
- Ligands
- ACE, GST, PPV, MG, NH2
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LYNF/TRUF/PATF family peptide O-prenyltransferase | protein | 296 | 36% helix, 30% strand | A0A372DCN7 |
| B | LYNF/TRUF/PATF family peptide O-prenyltransferase | protein | 294 | 35% helix, 29% strand | A0A372DCN7 |
| C | Substrate peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, C
- GST · Geranyl S-thiolodiphosphate · ligand · chains A, C
- PPV · Pyrophosphate · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NH2 · Amino group · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.73 | 0.81 | 62 | MG, PPV |
| 2 | 374 | 0.71 | 0.83 | 53 | MG, GST |
| 3 | 294 | 0.63 | 0.80 | 27 | empty |
| 4 | 224 | 0.56 | 0.78 | 22 | empty |
| 5 | 98 | 0.43 | 0.78 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 475 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 459 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7VMW · Crystal structure of LimF prenyltransferase bound with a peptide substrate and GSPP · 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
- Every structure of UniProt A0A372DCN7
- Elsewhere: RCSB PDB 7VMW · PDBe 7VMW · UniProt A0A372DCN7
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