Research workbench
Crystal structure of the N-terminal domain of oxytricha nova telomere end binding protein alpha subunit both uncomplexed and complexed with telomeric ssdna
Analyse Crystal structure of the N-terminal domain of oxytricha nova telomere end… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K8G
- Type
- protein + DNA
- Length
- 830 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(TP*TP*GP*GP*GP*G)-3'; Telomere-binding protein alpha subunit
- UniProt
- P29549
- Ligands
- SO4
- Pockets
- 16 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E | 5'-D(TP*TP*GP*GP*GP*G)-3' | dna | 4 | — | — |
| A | Telomere-binding protein alpha subunit | protein | 269 | 15% helix, 36% strand | P29549 |
| B | Telomere-binding protein alpha subunit | protein | 275 | 16% helix, 39% strand | P29549 |
| C | Telomere-binding protein alpha subunit | protein | 278 | 16% helix, 37% strand | P29549 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.48 | 0.78 | 21 | empty |
| 2 | 150 | 0.45 | 0.76 | 26 | empty |
| 3 | 123 | 0.42 | 0.76 | 24 | empty |
| 4 | 71 | 0.42 | 0.80 | 21 | empty |
| 5 | 73 | 0.38 | 0.78 | 24 | SO4 |
Interfaces
7 interfaces between chains.
- B–C · 621 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 574 Ų buried · 14 hydrogen bonds · protein-protein
- D–A · 554 Ų buried · 22 hydrogen bonds · protein-nucleic
- E–B · 549 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 457 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1K8G · Crystal Structure of the N-terminal domain of Oxytricha nova telomere end binding protein… · the same entry in another collection · chain C against C, TM-score 1.00
- P29549 · AlphaFold monomer V2.0 prediction for telomere-binding protein subunit alpha (P29549) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P29549
- Elsewhere: RCSB PDB 1K8G · PDBe 1K8G · UniProt P29549
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