Research workbench
Heterodimer crystal structure of geranylgeranyl diphosphate synthases 1 with ggpps recruiting PROTEIN(OSGRP) from oryza sativa
Analyse Heterodimer crystal structure of geranylgeranyl diphosphate synthases 1 with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XN6
- Type
- protein
- Length
- 1,627 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- OS07G0580900 protein; OS02G0668100 protein
- UniProt
- Q7XI92, Q6ET88
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 68% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | OS07G0580900 protein | protein | 281 | 70% helix, 1% strand | Q7XI92 |
| C | OS02G0668100 protein | protein | 262 | 61% helix, 0% strand | Q6ET88 |
| B | OS07G0580900 protein | protein | 277 | 70% helix, 1% strand | Q7XI92 |
| D | OS02G0668100 protein | protein | 266 | 67% helix, 0% strand | Q6ET88 |
| E | OS07G0580900 protein | protein | 278 | 71% helix, 1% strand | Q7XI92 |
| F | OS02G0668100 protein | protein | 263 | 70% helix, 0% strand | Q6ET88 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.78 | 0.83 | 56 | empty |
| 2 | 662 | 0.73 | 0.79 | 83 | empty |
| 3 | 698 | 0.72 | 0.78 | 58 | empty |
| 4 | 590 | 0.71 | 0.79 | 62 | empty |
| 5 | 341 | 0.71 | 0.83 | 39 | empty |
Interfaces
7 interfaces between chains.
- B–D · 1805 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 1780 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1741 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 519 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 512 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5XN6 · Heterodimer crystal structure of geranylgeranyl diphosphate synthases 1 with GGPPS… · 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 Q7XI92
- Every structure of UniProt Q6ET88
- Elsewhere: RCSB PDB 5XN6 · PDBe 5XN6 · UniProt Q7XI92 · UniProt Q6ET88
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