Research workbench
Crystal structure of yeast CDC13 and STN1
Analyse Crystal structure of yeast CDC13 and STN1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LBT
- Type
- protein
- Length
- 900 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- KLLA0F20922P,KLLA0F20922P; KLLA0C11825P
- UniProt
- Q6CJ70, Q6CTL1
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | KLLA0F20922P,KLLA0F20922P | protein | 295 | 24% helix, 34% strand | Q6CJ70 |
| C, D | KLLA0C11825P | protein | 151 | 52% helix, 19% strand | Q6CTL1 |
| B | KLLA0F20922P,KLLA0F20922P | protein | 303 | 24% helix, 34% strand | Q6CJ70 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.81 | 0.87 | 50 | empty |
| 2 | 552 | 0.81 | 0.87 | 55 | empty |
| 3 | 827 | 0.72 | 0.78 | 89 | empty |
| 4 | 240 | 0.67 | 0.84 | 30 | empty |
| 5 | 318 | 0.59 | 0.78 | 51 | empty |
Interfaces
5 interfaces between chains.
- A–C · 780 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 713 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 627 Ų buried · 3 hydrogen bonds · protein-protein
- C–B · 525 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 43 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6LBT · Crystal structure of yeast Cdc13 and Stn1 · the same entry in another collection · chain D against D, 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 Q6CJ70
- Every structure of UniProt Q6CTL1
- Elsewhere: RCSB PDB 6LBT · PDBe 6LBT · UniProt Q6CJ70 · UniProt Q6CTL1
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