Research workbench
TgoT_6G12 binary with 2 hCTPs
Analyse TgoT_6G12 binary with 2 hCTPs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B0G
- Type
- protein + DNA
- Length
- 759 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3
- Source
- Thermococcus gorgonarius; SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase; DNA (5'-D(P*GP*GP*AP*GP*GP*GP*CP*AP*GP*()P*())-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- P56689
- Ligands
- CTP, PO4
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · resolution 3 · 3 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 737 | 41% helix, 23% strand | P56689 |
| P | DNA (5'-D(P*GP*GP*AP*GP*GP*GP*CP*AP*GP*()P*())-3') | dna | 11 | — | — |
| T | DNA (5'-D(P*AP*TP*TP*GP*GP*CP*TP*GP*CP*CP*CP*TP*CP*C)-3') | dna | 11 | — | — |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · chains A, P
- PO4 · Phosphate ion · ion · 2 copies · chains T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.68 | 0.84 | 32 | empty |
| 2 | 476 | 0.64 | 0.77 | 54 | empty |
| 3 | 347 | 0.62 | 0.78 | 26 | empty |
| 4 | 306 | 0.61 | 0.79 | 32 | empty |
| 5 | 94 | 0.59 | 0.87 | 27 | CTP |
Interfaces
3 interfaces between chains.
- A–T · 828 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–P · 610 Ų buried · 11 hydrogen bonds · protein-nucleic
- P–T · 457 Ų buried · 43 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified, 1 disulfide (nucleotide modification, disulfide).
Compared structures
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 P56689
- Elsewhere: RCSB PDB 7B0G · PDBe 7B0G · UniProt P56689
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