MolNFT v1 · #128048 · protein
Crystal structure of variants
5NEZ · Geranylgeranylglyceryl phosphate synthase: “Crystal structure of variants”. X-ray diffraction, 11 pockets (best druggability 0.81). MolNFT v1 #128048 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5NEZ
- Type
- protein
- Length
- 1,445 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranylgeranylglyceryl phosphate synthase
- EC
- 2.5.1.41
- UniProt
- O26652
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 238 | 42% helix, 21% strand | O26652 |
| B | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 242 | 43% helix, 19% strand | O26652 |
| C | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 242 | 42% helix, 19% strand | O26652 |
| D | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 241 | 44% helix, 20% strand | O26652 |
| E | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 246 | 41% helix, 19% strand | O26652 |
| F | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 236 | 41% helix, 19% strand | O26652 |
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1155 | 0.81 | 0.82 | 98 | empty |
| 2 | 742 | 0.79 | 0.83 | 84 | empty |
| 3 | 592 | 0.79 | 0.85 | 76 | empty |
| 4 | 700 | 0.78 | 0.83 | 82 | empty |
| 5 | 729 | 0.78 | 0.82 | 88 | empty |
Interfaces
12 interfaces between chains.
- A–C · 1206 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1200 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 1193 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 825 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 811 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
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 O26652
- Elsewhere: RCSB PDB 5NEZ · PDBe 5NEZ · UniProt O26652
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