MolNFT v1 · #20788 · protein + DNA
T4 polynucleotide kinase bound to 5'-tgcac-3' ssdna
1RPZ · 5'-D(*TP*GP*CP*AP*C)-3': “T4 polynucleotide kinase bound to 5'-tgcac-3' ssdna”. X-ray diffraction, 2 ligands (ADP, CA), 3 pockets (best druggability 0.59). MolNFT v1 #20788 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1RPZ
- Type
- protein + DNA
- Length
- 290 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*GP*CP*AP*C)-3'; Polynucleotide kinase
- EC
- 2.7.1.78
- UniProt
- P06855
- Ligands
- ADP, CA
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*TP*GP*CP*AP*C)-3' | dna | 3 | — | — |
| A | Polynucleotide kinase (EC 2.7.1.78) | protein | 287 | 45% helix, 20% strand | P06855 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- CA · Calcium ion · metal · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.59 | 0.79 | 32 | ADP |
| 2 | 66 | 0.33 | 0.76 | 15 | empty |
| 3 | 58 | 0.27 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- B–A · 529 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1RPZ · T4 polynucleotide kinase bound to 5'-tgcac-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 1RPZ · PDBe 1RPZ · UniProt P06855
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