Research workbench
Tdt core in complex with inhibitor (2Z,5E)-6-[4-(4-fluorobenzoyl)-1H- pyrrol-2-yl]-2-hydroxy-4-oxohexa-2,5-dienoic acid and ssdna
Analyse Tdt core in complex with inhibitor (2Z,5E)-6-[4-(4-fluorobenzoyl)-1H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IQW
- Type
- protein + DNA
- Length
- 360 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA nucleotidylexotransferase; 5'-D(*GP*CP*CP*G)-3'
- EC
- 2.7.7.31
- UniProt
- P09838
- Ligands
- 1FQ, NA
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA nucleotidylexotransferase (EC 2.7.7.31) | protein | 357 | 50% helix, 15% strand | P09838 |
| C | 5'-D(*GP*CP*CP*G)-3' | dna | 3 | — | — |
Ligands and binding sites
- 1FQ · (2Z,5E)-6-[4-(4-fluorobenzoyl)-1H-pyrrol-2-yl]-2-hydroxy-4-oxohexa-2,5-dienoic acid · ligand · chains A
- NA · Sodium ion · metal · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.73 | 0.76 | 73 | NA, 1FQ |
Interfaces
1 interface between chains.
- A–C · 320 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 4IQW · Tdt core in complex with inhibitor (2Z,5E)-6-[4-(4-fluorobenzoyl)-1H-pyrrol-2-yl]-2-hydrox… · the same entry in another collection · chain A against A, TM-score 1.00
- P09838 · AlphaFold monomer V2.0 prediction for DNA nucleotidylexotransferase (P09838) · a predicted model of the same protein · chain A against A, 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 P09838
- Elsewhere: RCSB PDB 4IQW · PDBe 4IQW · UniProt P09838
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