Research workbench
DNA G-quartets in a 1.86 a resolution structure of an oxytricha nova telomeric protein-DNA complex
Analyse DNA G-quartets in a 1.86 a resolution structure of an oxytricha nova telomeric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JB7
- Type
- protein + DNA
- Length
- 712 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'; Telomere-binding protein alpha subunit…
- UniProt
- P29549, P16458
- Ligands
- NA, CL
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, G, H | 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3' | dna | 12 | — | — |
| A | Telomere-binding protein alpha subunit | protein | 460 | 19% helix, 38% strand | P29549 |
| B | Telomere-binding protein beta subunit | protein | 216 | 33% helix, 23% strand | P16458 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.84 | 0.94 | 35 | empty |
| 2 | 593 | 0.70 | 0.79 | 66 | empty |
| 3 | 460 | 0.58 | 0.74 | 44 | empty |
| 4 | 156 | 0.50 | 0.78 | 20 | empty |
| 5 | 95 | 0.43 | 0.78 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2702 Ų buried · 44 hydrogen bonds · protein-protein
- D–A · 1223 Ų buried · 32 hydrogen bonds · protein-nucleic
- G–H · 795 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- D–B · 411 Ų buried · 10 hydrogen bonds · protein-nucleic
- G–A · 196 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 1JB7 · DNA G-Quartets in a 1.86 A Resolution Structure of an Oxytricha nova Telomeric… · the same entry in another collection · chain G against G, TM-score 1.00
- P16458 · AlphaFold monomer V2.0 prediction for telomere-binding protein subunit beta (P16458) · a predicted model of the same protein · chain B against A, 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
- Every structure of UniProt P16458
- Elsewhere: RCSB PDB 1JB7 · PDBe 1JB7 · UniProt P29549 · UniProt P16458
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