MolNFT v1 · #154354 · protein
Crystal structure of arabidopsis thaliana BIC2-CRY2 complex
6K8K · Cryptochrome-2: “Crystal structure of arabidopsis thaliana BIC2-CRY2 complex”. X-ray diffraction, 3 ligands (FAD, AMP, MG), 20 pockets (best druggability 0.82). MolNFT v1 #154354 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6K8K
- Type
- protein
- Length
- 2,160 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cryptochrome-2; Protein BIC2
- UniProt
- Q96524, Q9M280
- Ligands
- FAD, AMP, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 55% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cryptochrome-2 | protein | 484 | 54% helix, 7% strand | Q96524 |
| E | Protein BIC2 | protein | 55 | 58% helix, 0% strand | Q9M280 |
| B | Cryptochrome-2 | protein | 481 | 55% helix, 7% strand | Q96524 |
| C | Protein BIC2 | protein | 51 | 55% helix, 0% strand | Q9M280 |
| D | Cryptochrome-2 | protein | 486 | 55% helix, 7% strand | Q96524 |
| F | Protein BIC2 | protein | 56 | 55% helix, 0% strand | Q9M280 |
| G | Cryptochrome-2 | protein | 490 | 55% helix, 7% strand | Q96524 |
| H | Protein BIC2 | protein | 57 | 54% helix, 0% strand | Q9M280 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, D, G
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, D, G
- MG · Magnesium ion · metal · 4 copies · chains A, D, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.82 | 0.86 | 49 | FAD, AMP |
| 2 | 725 | 0.81 | 0.85 | 55 | FAD, AMP, MG |
| 3 | 701 | 0.81 | 0.85 | 49 | FAD, AMP, MG |
| 4 | 681 | 0.81 | 0.85 | 49 | FAD, AMP |
| 5 | 117 | 0.79 | 0.98 | 26 | empty |
Interfaces
8 interfaces between chains.
- D–F · 2416 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2344 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 2210 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 2125 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1995 Ų buried · 20 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 Q96524
- Every structure of UniProt Q9M280
- Elsewhere: RCSB PDB 6K8K · PDBe 6K8K · UniProt Q96524 · UniProt Q9M280
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