MolNFT v1 · #149523 · protein
Crystal structure of human geranylgeranyl diphosphate synthase mutant D188Y
6G32 · Geranylgeranyl pyrophosphate synthase: “Crystal structure of human geranylgeranyl diphosphate synthase mutant D188Y”. X-ray diffraction, 19 pockets (best druggability 0.81). MolNFT v1 #149523 on GenesisL1: 3D structure, binding…
- PDB
- 6G32
- Type
- protein
- Length
- 1,709 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
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 76% 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 | 286 | 77% 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 | 285 | 77% 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 | 285 | 75% 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 | 284 | 77% 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 | 284 | 75% 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 | 285 | 76% helix, 1% strand | O95749 |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.81 | 0.82 | 104 | GOL |
| 2 | 924 | 0.81 | 0.82 | 88 | GOL |
| 3 | 778 | 0.78 | 0.82 | 65 | GOL |
| 4 | 787 | 0.78 | 0.82 | 73 | GOL |
| 5 | 872 | 0.76 | 0.80 | 69 | GOL |
Interfaces
7 interfaces between chains.
- A–B · 1640 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 1627 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1610 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 438 Ų buried · 0 hydrogen bonds · protein-protein
- C–F · 433 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6G32 · Crystal structure of human geranylgeranyl diphosphate synthase mutant D188Y · the same entry in another collection · chain F against F, 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 0.99
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 6G32 · PDBe 6G32 · UniProt O95749
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