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Structure analysis of geranyl diphosphate methyltransferase in complex with gpp and sinefungin
Analyse Structure analysis of geranyl diphosphate methyltransferase in complex with gpp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F86
- Type
- protein
- Length
- 3,249 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranyl diphosphate 2-C-methyltransferase
- EC
- 2.1.1.-
- UniProt
- D3KYU3
- Ligands
- SFG, GPP, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 12 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 275 | 43% helix, 20% strand | D3KYU3 |
| B | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 273 | 45% helix, 21% strand | D3KYU3 |
| C | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 274 | 44% helix, 20% strand | D3KYU3 |
| D | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 273 | 44% helix, 21% strand | D3KYU3 |
| E | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 272 | 45% helix, 21% strand | D3KYU3 |
| F | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 269 | 44% helix, 21% strand | D3KYU3 |
| G | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 269 | 45% helix, 21% strand | D3KYU3 |
| H | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 268 | 43% helix, 21% strand | D3KYU3 |
| I | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 273 | 44% helix, 21% strand | D3KYU3 |
| J | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 272 | 44% helix, 21% strand | D3KYU3 |
| K | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 258 | 41% helix, 22% strand | D3KYU3 |
| L | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 273 | 42% helix, 21% strand | D3KYU3 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- GPP · Geranyl diphosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.86 | 0.87 | 134 | SFG, GPP, MG |
| 2 | 247 | 0.84 | 0.96 | 54 | SFG, GPP, MG |
| 3 | 233 | 0.84 | 0.97 | 49 | SFG, GPP, MG |
| 4 | 232 | 0.84 | 0.97 | 49 | SFG, GPP |
| 5 | 1058 | 0.84 | 0.85 | 125 | SFG, GPP |
Interfaces
26 interfaces between chains.
- A–F · 1061 Ų buried · 27 hydrogen bonds · protein-protein
- J–K · 1048 Ų buried · 25 hydrogen bonds · protein-protein
- G–L · 1048 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1045 Ų buried · 27 hydrogen bonds · protein-protein
- H–I · 1045 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4F86 · Structure analysis of Geranyl diphosphate methyltransferase in complex with GPP and… · the same entry in another collection · chain J against J, 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 D3KYU3
- Elsewhere: RCSB PDB 4F86 · PDBe 4F86 · UniProt D3KYU3
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