Research workbench
Versatile cis-prenyltransferase MM_0014 from methanosarcina mazei (crystal type: co-fg)
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
- 7CC3
- Type
- protein
- Length
- 1,700 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cis-prenyltransferase MM_0014
- Ligands
- FQ0, FQF, FV3, DPO, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cis-prenyltransferase MM_0014 | protein | 211 | 39% helix, 18% strand | — |
| B | Cis-prenyltransferase MM_0014 | protein | 221 | 39% helix, 17% strand | — |
| C | Cis-prenyltransferase MM_0014 | protein | 216 | 41% helix, 18% strand | — |
| D | Cis-prenyltransferase MM_0014 | protein | 206 | 41% helix, 18% strand | — |
| E | Cis-prenyltransferase MM_0014 | protein | 215 | 40% helix, 19% strand | — |
| F | Cis-prenyltransferase MM_0014 | protein | 204 | 40% helix, 19% strand | — |
| G | Cis-prenyltransferase MM_0014 | protein | 207 | 40% helix, 18% strand | — |
| H | Cis-prenyltransferase MM_0014 | protein | 220 | 40% helix, 17% strand | — |
Ligands and binding sites
- FQ0 · 2-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propane-1,3-diol · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- FQF · (2R)-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propane-1,2-diol · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- FV3 · (2S)-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propane-1,2-diol · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- DPO · Diphosphate · ligand · 3 copies · chains B, E, G
- PO4 · Phosphate ion · ion · 5 copies · chains A, C, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.82 | 0.92 | 54 | PO4, FQ0, FQF, FV3 |
| 2 | 1181 | 0.81 | 0.82 | 127 | PO4, FQ0, FQF, FV3 |
| 3 | 1175 | 0.81 | 0.82 | 95 | PO4, FQ0, FQF, FV3 |
| 4 | 319 | 0.80 | 0.91 | 49 | DPO, FQ0, FQF, FV3 |
| 5 | 303 | 0.80 | 0.91 | 55 | PO4, FQ0, FQF, FV3 |
Interfaces
11 interfaces between chains.
- G–H · 1598 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1550 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1524 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1450 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 617 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7CC3 · Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: co-FG) · 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 7CC3 · PDBe 7CC3
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