Research workbench
T4 polynucleotide kinase bound to 5'-gtcac-3' ssdna
Analyse T4 polynucleotide kinase bound to 5'-gtcac-3' ssdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RC8
- Type
- protein + DNA
- Length
- 292 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*TP*CP*AP*C)-3'; Polynucleotide kinase
- EC
- 2.7.1.78
- UniProt
- P06855
- Ligands
- ADP, CA
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*GP*TP*CP*AP*C)-3' | dna | 3 | — | — |
| A | Polynucleotide kinase (EC 2.7.1.78) | protein | 289 | 43% helix, 19% strand | P06855 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- CA · Calcium ion · metal · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.51 | 0.78 | 28 | ADP |
| 2 | 70 | 0.30 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- B–A · 546 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1RC8 · T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA · the same entry in another collection · chain B against B, 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 P06855
- Elsewhere: RCSB PDB 1RC8 · PDBe 1RC8 · UniProt P06855
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