Research workbench
Kaicba circadian clock backbone model based on a cryo-EM density
Analyse Kaicba circadian clock backbone model based on a cryo-EM density in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N8Y
- Type
- protein
- Length
- 4,752 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Circadian clock protein kinase kaic; Circadian clock protein kaib; Circadian clock…
- EC
- 2.7.11.1
- UniProt
- Q79PF4, Q79PF5, Q79PF6
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 483 | 32% helix, 24% strand | Q79PF4 |
| G, H, K, J, I, L | Circadian clock protein kaib | protein | 93 | 42% helix, 24% strand | Q79PF5 |
| M, O, Q, S, U, X | Circadian clock protein kaia | protein | 109 | 72% helix, 0% strand | Q79PF6 |
| N, P, R, T, V, W | Circadian clock protein kaia | protein | 107 | 81% helix, 0% strand | Q79PF6 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.83 | 0.85 | 121 | empty |
| 2 | 1159 | 0.82 | 0.83 | 137 | empty |
| 3 | 1194 | 0.82 | 0.83 | 146 | empty |
| 4 | 1148 | 0.82 | 0.83 | 134 | empty |
| 5 | 941 | 0.81 | 0.83 | 131 | empty |
Interfaces
24 interfaces between chains.
- B–C · 832 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 831 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 819 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 809 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 808 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5N8Y · KaiCBA circadian clock backbone model based on a Cryo-EM density · the same entry in another collection · chain J against J, 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 Q79PF4
- Every structure of UniProt Q79PF5
- Every structure of UniProt Q79PF6
- Elsewhere: RCSB PDB 5N8Y · PDBe 5N8Y · UniProt Q79PF4 · UniProt Q79PF5 · UniProt Q79PF6
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