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Crystal structure of variants
Analyse Crystal structure of variants in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NF1
- Type
- protein
- Length
- 1,372 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 0.88
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 233 | 40% helix, 21% strand | O26652 |
| B | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 221 | 37% helix, 22% strand | O26652 |
| C | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 226 | 38% helix, 19% strand | O26652 |
| D | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 224 | 38% helix, 21% strand | O26652 |
| E | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 237 | 38% helix, 19% strand | O26652 |
| F | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 231 | 39% helix, 20% 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 | 1161 | 0.88 | 0.90 | 185 | empty |
| 2 | 411 | 0.80 | 0.88 | 53 | empty |
| 3 | 259 | 0.80 | 0.92 | 53 | empty |
| 4 | 255 | 0.79 | 0.91 | 42 | empty |
| 5 | 263 | 0.78 | 0.90 | 41 | empty |
Interfaces
12 interfaces between chains.
- B–D · 1173 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 1172 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 1168 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 814 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 745 Ų buried · 7 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 5NF1 · PDBe 5NF1 · UniProt O26652
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