Research workbench
Mint heterotetrameric geranyl pyrophosphate synthase in complex with magnesium, ipp, and dmaspp (II)
Analyse Mint heterotetrameric geranyl pyrophosphate synthase in complex with magnesium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KRO
- Type
- protein
- Length
- 1,092 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranyl diphosphate synthase large subunit; Geranyl diphosphate synthase small subunit
- EC
- 2.5.1.1
- UniProt
- Q9SBR3, Q9SBR4
- Ligands
- IPE, PPV, DST, MG
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranyl diphosphate synthase large subunit (EC 2.5.1.1) | protein | 279 | 75% helix, 1% strand | Q9SBR3 |
| B, C | Geranyl diphosphate synthase small subunit (EC 2.5.1.1) | protein | 259 | 67% helix, 0% strand | Q9SBR4 |
| D | Geranyl diphosphate synthase large subunit (EC 2.5.1.1) | protein | 295 | 75% helix, 1% strand | Q9SBR3 |
Ligands and binding sites
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · 2 copies · chains A, D
- PPV · Pyrophosphate · ligand · chains A
- DST · Dimethylallyl S-thiolodiphosphate · ligand · chains D
- MG · Magnesium ion · metal · 4 copies · chains A, D
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.81 | 0.91 | 46 | IPE, DST, MG |
| 2 | 397 | 0.70 | 0.82 | 52 | empty |
| 3 | 366 | 0.66 | 0.80 | 36 | empty |
| 4 | 376 | 0.62 | 0.77 | 37 | IPE, PPV |
| 5 | 404 | 0.61 | 0.76 | 57 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2089 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2012 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 474 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 435 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 85 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3KRO · Mint heterotetrameric geranyl pyrophosphate synthase in complex with magnesium, IPP, and… · 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
- Every structure of UniProt Q9SBR3
- Every structure of UniProt Q9SBR4
- Elsewhere: RCSB PDB 3KRO · PDBe 3KRO · UniProt Q9SBR3 · UniProt Q9SBR4
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