MolNFT v1 · #162303 · protein
Crystal structure of human geranylgeranyl diphosphate synthase bound to ibandronate
6R4V · Geranylgeranyl pyrophosphate synthase: “Crystal structure of human geranylgeranyl diphosphate synthase bound to ibandronate”. X-ray diffraction, 2 ligands (BFQ, MG), 20 pockets (best druggability 0.82). MolNFT v1 #162303 on…
- PDB
- 6R4V
- Type
- protein
- Length
- 1,733 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranylgeranyl pyrophosphate synthase
- EC
- 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10
- UniProt
- O95749
- Ligands
- BFQ, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 288 | 75% helix, 1% strand | O95749 |
| C | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 294 | 74% helix, 1% strand | O95749 |
| F | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 286 | 76% helix, 1% strand | O95749 |
| E | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 288 | 76% helix, 1% strand | O95749 |
| B | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 290 | 76% helix, 1% strand | O95749 |
| D | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 287 | 76% helix, 1% strand | O95749 |
Ligands and binding sites
- BFQ · Ibandronate · ligand · 6 copies · chains A, C, F, E, B, D
- MG · Magnesium ion · metal · 17 copies · chains A, C, F, E, B, D
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 759 | 0.82 | 0.85 | 65 | MG, BFQ |
| 2 | 641 | 0.81 | 0.86 | 57 | MG, BFQ |
| 3 | 720 | 0.81 | 0.85 | 70 | MG, BFQ |
| 4 | 741 | 0.81 | 0.85 | 63 | MG, BFQ |
| 5 | 481 | 0.79 | 0.87 | 50 | MG, BFQ, GOL |
Interfaces
12 interfaces between chains.
- C–D · 1639 Ų buried · 9 hydrogen bonds · protein-protein
- F–E · 1613 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1602 Ų buried · 8 hydrogen bonds · protein-protein
- C–B · 499 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 487 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6R4V · Crystal structure of human geranylgeranyl diphosphate synthase bound to ibandronate · the same entry in another collection · chain D against D, TM-score 1.00
- O95749 · AlphaFold monomer V2.0 prediction for geranylgeranyl pyrophosphate synthase (O95749) · a predicted model of the same protein · 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 O95749
- Elsewhere: RCSB PDB 6R4V · PDBe 6R4V · UniProt O95749
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