Research workbench
Crystal structure of the replication termination protein in complex with a pseudosymmetric B-site
Analyse Crystal structure of the replication termination protein in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DPD
- Type
- protein + DNA
- Length
- 274 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*AP*AP*TP*GP*TP*TP*CP*AP *TP*AP*G)-3'…
- UniProt
- P68732
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*AP*AP*TP*GP*TP*TP*CP*AP *TP*AP*G)-3' | dna | 21 | — | — |
| E | 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*TP*AP*TP*GP*TP*TP*CP*AP *TP*AP*G)-3' | dna | 21 | — | — |
| A | Replication termination protein | protein | 115 | 59% helix, 9% strand | P68732 |
| B | Replication termination protein | protein | 117 | 58% helix, 11% strand | P68732 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.67 | 0.83 | 40 | empty |
| 2 | 96 | 0.44 | 0.79 | 13 | empty |
| 3 | 104 | 0.40 | 0.77 | 15 | empty |
| 4 | 54 | 0.32 | 0.77 | 11 | empty |
| 5 | 79 | 0.29 | 0.72 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1783 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 921 Ų buried · 85 hydrogen bonds · nucleic-nucleic
- D–B · 596 Ų buried · 11 hydrogen bonds · protein-nucleic
- E–A · 519 Ų buried · 11 hydrogen bonds · protein-nucleic
- E–B · 478 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 2DPD · Crystal structure of the Replication Termination Protein in complex with a… · the same entry in another collection · chain D against D, 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
- Every structure of UniProt P68732
- Elsewhere: RCSB PDB 2DPD · PDBe 2DPD · UniProt P68732
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.