MolNFT v1 · #174926 · protein
Versatile cis-prenyltransferase MM_0014 from methanosarcina mazei (crystal type: co-FG+DMAPP)
7CAV: “Versatile cis-prenyltransferase MM_0014 from methanosarcina mazei (crystal type: co-FG+DMAPP)”. X-ray diffraction, 5 ligands (DMA, DPO, FQ0), 20 pockets (best druggability 0.84). MolNFT v1 #174926 on GenesisL1: 3D structure, binding…
- PDB
- 7CAV
- Type
- protein
- Length
- 1,706 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cis-prenyltransferase MM_0014
- Ligands
- DMA, DPO, FQ0, MG, PO4
- Pockets
- 20 · best druggability 0.84
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, 19% strand | — |
| B | Cis-prenyltransferase MM_0014 | protein | 222 | 39% helix, 17% strand | — |
| C | Cis-prenyltransferase MM_0014 | protein | 217 | 41% helix, 16% strand | — |
| D | Cis-prenyltransferase MM_0014 | protein | 211 | 39% helix, 18% strand | — |
| E | Cis-prenyltransferase MM_0014 | protein | 204 | 41% helix, 20% strand | — |
| F | Cis-prenyltransferase MM_0014 | protein | 216 | 42% helix, 19% strand | — |
| G | Cis-prenyltransferase MM_0014 | protein | 219 | 40% helix, 17% strand | — |
| H | Cis-prenyltransferase MM_0014 | protein | 206 | 40% helix, 18% strand | — |
Ligands and binding sites
- DMA · Dimethylallyl diphosphate · ligand · 8 copies · chains A, B, C, D, E, F
- DPO · Diphosphate · ligand · 7 copies · chains B, F, G, A, H
- FQ0 · 2-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propane-1,3-diol · ligand · 4 copies · chains B, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- PO4 · Phosphate ion · ion · chains G, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.84 | 0.95 | 41 | DMA, MG |
| 2 | 276 | 0.83 | 0.94 | 38 | DMA, MG |
| 3 | 268 | 0.83 | 0.94 | 40 | DMA, MG |
| 4 | 895 | 0.83 | 0.84 | 86 | MG, FQ0, DPO |
| 5 | 452 | 0.82 | 0.90 | 65 | DMA, MG |
Interfaces
11 interfaces between chains.
- C–D · 1751 Ų buried · 32 hydrogen bonds · protein-protein
- G–H · 1571 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1555 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1519 Ų buried · 22 hydrogen bonds · protein-protein
- C–F · 597 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7CAV · Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type… · the same entry in another collection · chain G against G, 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 7CAV · PDBe 7CAV
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