MolNFT v1 · #98642 · protein
Crystal structure of geranylgeranyl diphosphate synthase SUB1274 (target efi-509455) from streptococcus uberis 0140J with bound magnesium and isopentyl diphosphate, partially liganded complex;
4LFE: “Crystal structure of geranylgeranyl diphosphate synthase SUB1274 (target efi-509455) from streptococcus…”. X-ray diffraction, 2 ligands (IPE, MG), 3 pockets (best druggability 0.77). MolNFT v1 #98642 on GenesisL1: 3D structure…
- PDB
- 4LFE
- Type
- protein
- Length
- 562 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranylgeranyl diphosphate synthase
- EC
- 2.5.1.10
- UniProt
- B9DUT7
- Ligands
- IPE, MG
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranylgeranyl diphosphate synthase (EC 2.5.1.10) | protein | 274 | 72% helix, 1% strand | B9DUT7 |
| B | Geranylgeranyl diphosphate synthase (EC 2.5.1.10) | protein | 288 | 71% helix, 1% strand | B9DUT7 |
Ligands and binding sites
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · 3 copies · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.77 | 0.89 | 42 | IPE, MG |
| 2 | 479 | 0.69 | 0.79 | 50 | IPE, MG |
| 3 | 57 | 0.30 | 0.75 | 9 | empty |
Interfaces
1 interface between chains.
- A–B · 2215 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4LFE · Crystal structure of geranylgeranyl diphosphate synthase sub1274 (target efi-509455) from… · 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 B9DUT7
- Elsewhere: RCSB PDB 4LFE · PDBe 4LFE · UniProt B9DUT7
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