Research workbench
X-ray data do not support hoogsteen base-pairing during replication by human polymerase iota
Analyse X-ray data do not support hoogsteen base-pairing during replication by human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZET
- Type
- protein + DNA
- Length
- 415 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*AP*GP*GP*GP*(BRU)P*CP*CP*(BRU)P*(BRU) P*CP*CP*CP*CP*C)-3'…
- Ligands
- TTP, MG
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | 5'-D(P*AP*GP*GP*GP*(BRU)P*CP*CP*(BRU)P*(BRU) P*CP*CP*CP*CP*C)-3' | dna | 14 | — | — |
| P | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*(DOC))-3' | dna | 13 | — | — |
| A | Polymerase (DNA directed) iota | protein | 388 | 40% helix, 13% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.78 | 0.81 | 81 | TTP |
| 2 | 501 | 0.71 | 0.81 | 43 | empty |
| 3 | 145 | 0.57 | 0.82 | 20 | empty |
| 4 | 169 | 0.49 | 0.77 | 18 | empty |
| 5 | 74 | 0.31 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- T–A · 818 Ų buried · 18 hydrogen bonds · protein-nucleic
- P–A · 748 Ų buried · 31 hydrogen bonds · protein-nucleic
- T–P · 592 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 1ZET · X-ray data do not support hoogsteen base-pairing during replication by human polymerase… · the same entry in another collection · chain T against T, 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
- Elsewhere: RCSB PDB 1ZET · PDBe 1ZET
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.