MolNFT v1 · #82096 · protein
Crystal structure of geranyl diphosphate C-methyltransferase from streptomyces coelicolor A3(2) in complex with MG2+, geranyl-S- thiolodiphosphate, and S-adenosyl-L-homocysteine
3VC1 · Geranyl diphosphate 2-C-methyltransferase: “Crystal structure of geranyl diphosphate C-methyltransferase from streptomyces coelicolor A3(2) in complex…”. X-ray diffraction, 4 ligands (SAH, GST, MG), 20 pockets (best druggability…
- PDB
- 3VC1
- Type
- protein
- Length
- 3,343 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, GST, MG, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 277 | 44% helix, 20% strand | Q9F1Y5 |
| B, C, E, F, G, H, I, K, L | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 278 | 44% helix, 20% strand | Q9F1Y5 |
| D | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 288 | 44% helix, 19% strand | Q9F1Y5 |
| J | Geranyl diphosphate 2-C-methyltransferase (EC 2.1.1.-) | protein | 276 | 44% helix, 20% 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
- GST · Geranyl S-thiolodiphosphate · 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
- SO4 · Sulfate ion · ion · chains E, H
- GOL · Glycerol · additive · 15 copies · chains A, B, E, D, F, C, H, G, J, L, K, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.85 | 0.97 | 52 | MG, SAH, GST |
| 2 | 248 | 0.85 | 0.96 | 51 | MG, SAH, GST |
| 3 | 250 | 0.84 | 0.96 | 53 | MG, SAH, GST |
| 4 | 243 | 0.84 | 0.96 | 52 | MG, SAH, GST |
| 5 | 247 | 0.84 | 0.96 | 51 | MG, SAH, GST |
Interfaces
25 interfaces between chains.
- A–D · 1051 Ų buried · 30 hydrogen bonds · protein-protein
- I–L · 1032 Ų buried · 29 hydrogen bonds · protein-protein
- B–E · 1025 Ų buried · 30 hydrogen bonds · protein-protein
- C–F · 1020 Ų buried · 29 hydrogen bonds · protein-protein
- H–K · 1017 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3VC1 · 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 3VC1 · PDBe 3VC1 · UniProt Q9F1Y5
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