MolNFT v1 · #12328 · protein + DNA
Binary complex of murine terminal deoxynucleotidyl transferase with a primer single stranded DNA
1KDH · 5'-D(P*(BRU)P*(BRU)P*(BRU)P*(BRU))-3': “Binary complex of murine terminal deoxynucleotidyl transferase with a primer single stranded DNA”. X-ray diffraction, 2 ligands (MG, NA), 2 pockets (best druggability 0.71). MolNFT v1 #12328…
- PDB
- 1KDH
- Type
- protein + DNA
- Length
- 360 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*(BRU)P*(BRU)P*(BRU)P*(BRU))-3'; Terminal deoxynucleotidyltransferase short isoform
- EC
- 2.7.7.31
- Ligands
- MG, NA
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'-D(P*(BRU)P*(BRU)P*(BRU)P*(BRU))-3' | dna | 4 | — | — |
| A | Terminal deoxynucleotidyltransferase short isoform (EC 2.7.7.31) | protein | 356 | 48% helix, 15% strand | — |
Ligands and binding sites
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 | 867 | 0.71 | 0.76 | 59 | NA |
| 2 | 108 | 0.42 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- D–A · 631 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 1KDH · Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with a Primer Single… · 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
- Elsewhere: RCSB PDB 1KDH · PDBe 1KDH
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