Research workbench
Versatile cis-prenyltransferase MM_0014 from methanosarcina mazei (crystal type: FREE+IPP)
Analyse Versatile cis-prenyltransferase MM_0014 from methanosarcina mazei (crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CAR
- Type
- protein
- Length
- 411 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cis-prenyltransferase, MM_0014
- Ligands
- IPE, PLM, PO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cis-prenyltransferase, MM_0014 | protein | 214 | 41% helix, 18% strand | — |
| B | Cis-prenyltransferase, MM_0014 | protein | 197 | 42% helix, 18% strand | — |
Ligands and binding sites
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · chains A, B
- PLM · Palmitic acid · ligand · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.81 | 0.96 | 36 | PLM, PO4 |
| 2 | 276 | 0.76 | 0.89 | 45 | IPE, PO4 |
| 3 | 61 | 0.31 | 0.76 | 17 | empty |
| 4 | 71 | 0.30 | 0.74 | 13 | empty |
| 5 | 60 | 0.30 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1515 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 7CAR · Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: free+IPP) · the same entry in another collection · chain B against B, 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 7CAR · PDBe 7CAR
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