Research workbench
Crystal structure of geranyl diphosphate C-methyltransferase from streptomyces coelicolor A3(2) in complex with MG2+, geranyl diphosphate, and S-adenosyl-L-homocysteine
Analyse Crystal structure of geranyl diphosphate C-methyltransferase from streptomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VC2
- Type
- protein
- Length
- 3,287 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
- Q9F1Y5
- Ligands
- SAH, GPP, MG, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 10 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, H | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 277 | 44% helix, 20% strand | Q9F1Y5 |
| B | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 267 | 43% helix, 21% strand | Q9F1Y5 |
| C | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 267 | 43% helix, 21% strand | Q9F1Y5 |
| D | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 288 | 45% helix, 19% strand | Q9F1Y5 |
| F | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 273 | 43% helix, 21% strand | Q9F1Y5 |
| G | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 278 | 45% helix, 20% strand | Q9F1Y5 |
| I | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 276 | 45% helix, 20% strand | Q9F1Y5 |
| J | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 275 | 45% helix, 20% strand | Q9F1Y5 |
| K | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 263 | 44% helix, 21% strand | Q9F1Y5 |
| L | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 269 | 43% helix, 21% strand | Q9F1Y5 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- GPP · Geranyl diphosphate · ligand · 4 copies · chains A, D, H, J
- MG · Magnesium ion · metal · 4 copies · chains A, D, H, J
- SO4 · Sulfate ion · ion · chains E, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.84 | 0.97 | 45 | SAH |
| 2 | 302 | 0.84 | 0.94 | 58 | SAH |
| 3 | 236 | 0.84 | 0.96 | 52 | MG, SAH, GPP |
| 4 | 243 | 0.84 | 0.96 | 51 | MG, SAH, GPP |
| 5 | 248 | 0.84 | 0.96 | 54 | MG, SAH, GPP |
Interfaces
25 interfaces between chains.
- A–D · 1025 Ų buried · 29 hydrogen bonds · protein-protein
- I–L · 1018 Ų buried · 29 hydrogen bonds · protein-protein
- B–E · 1012 Ų buried · 28 hydrogen bonds · protein-protein
- G–J · 999 Ų buried · 27 hydrogen bonds · protein-protein
- C–F · 998 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3VC2 · Crystal structure of geranyl diphosphate C-methyltransferase from Streptomyces coelicolor… · the same entry in another collection · chain L against L, 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 Q9F1Y5
- Elsewhere: RCSB PDB 3VC2 · PDBe 3VC2 · UniProt Q9F1Y5
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