MolNFT v1 · #18193 · protein + DNA
Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssdna ggggttttggtg
1PH3 · 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, 1 ligand (NA), 11 pockets (best druggability 0.84). MolNFT…
- PDB
- 1PH3
- 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*GP*T)-3'…
- UniProt
- P29549, P16458
- Ligands
- NA
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 24% 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*GP*TP*G)-3' | dna | 12 | — | — |
| A | Telomere-binding protein alpha subunit | protein | 460 | 20% helix, 38% strand | P29549 |
| B | Telomere-binding protein beta subunit | protein | 216 | 32% helix, 23% strand | P16458 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains G, H
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 | 355 | 0.84 | 0.94 | 36 | empty |
| 2 | 559 | 0.70 | 0.79 | 66 | empty |
| 3 | 498 | 0.60 | 0.75 | 49 | empty |
| 4 | 148 | 0.51 | 0.79 | 24 | empty |
| 5 | 113 | 0.43 | 0.77 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2679 Ų buried · 46 hydrogen bonds · protein-protein
- D–A · 1188 Ų buried · 29 hydrogen bonds · protein-nucleic
- G–H · 794 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- D–B · 412 Ų buried · 13 hydrogen bonds · protein-nucleic
- G–A · 201 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 1PH3 · Crystal structure of the oxytricha nova telomere end-binding protein complexed with… · the same entry in another collection · chain D against D, 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 1PH3 · PDBe 1PH3 · UniProt P29549 · UniProt P16458
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