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
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
- 4IQU
- Type
- protein
- Length
- 358 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA nucleotidylexotransferase
- EC
- 2.7.7.31
- UniProt
- P09838
- Ligands
- 1FQ, NA
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA nucleotidylexotransferase (EC 2.7.7.31) | protein | 358 | 50% helix, 14% strand | P09838 |
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
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 | 623 | 0.66 | 0.76 | 57 | 1FQ |
| 2 | 62 | 0.36 | 0.78 | 14 | empty |
| 3 | 99 | 0.34 | 0.73 | 13 | empty |
Compared structures
- 4IQU · 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 4IQU · PDBe 4IQU · UniProt P09838
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