MolNFT v1 · #18195 · protein + DNA
Crystal structure of the oxytricha nova telomere end- binding protein complexed with noncognate ssdna GGGGTTTTG(3DR)GG
1PH5 · 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*T)-3': “Crystal structure of the oxytricha nova telomere end- binding protein complexed with noncognate ssdna…”. X-ray diffraction, 2 ligands (NA, CL), 11 pockets (best druggability 0.83).…
- PDB
- 1PH5
- Type
- protein + DNA
- Length
- 710 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*GP*T)-3'…
- UniProt
- P29549, P16458
- Ligands
- NA, CL
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, H | 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*T)-3' | dna | 12 | — | — |
| D | 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*(3DR)P*GP*G)-3' | dna | 11 | — | — |
| A | Telomere-binding protein alpha subunit | protein | 459 | 19% helix, 38% strand | P29549 |
| B | Telomere-binding protein beta subunit | protein | 216 | 31% helix, 23% strand | P16458 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.83 | 0.87 | 72 | empty |
| 2 | 508 | 0.66 | 0.78 | 52 | empty |
| 3 | 500 | 0.60 | 0.75 | 50 | empty |
| 4 | 172 | 0.56 | 0.80 | 22 | empty |
| 5 | 103 | 0.45 | 0.78 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2671 Ų buried · 47 hydrogen bonds · protein-protein
- D–A · 1138 Ų buried · 27 hydrogen bonds · protein-nucleic
- G–H · 792 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- D–B · 299 Ų buried · 7 hydrogen bonds · protein-nucleic
- G–A · 198 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1PH5 · Crystal structure of the oxytricha nova telomere end-binding protein complexed with… · 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 0.99
- 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 1PH5 · PDBe 1PH5 · UniProt P29549 · UniProt P16458
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