MolNFT v1 · #91860 · protein + DNA
Crystal structure of D. rerio TDP2 complexed with single strand DNA product
4FPV · Tyrosyl-DNA phosphodiesterase 2: “Crystal structure of D. rerio TDP2 complexed with single strand DNA product”. X-ray diffraction, 2 ligands (NA, MG), 2 pockets (best druggability 0.80). MolNFT v1 #91860 on GenesisL1: 3D structure…
- PDB
- 4FPV
- Type
- protein + DNA
- Length
- 512 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-DNA phosphodiesterase 2; DNA (5'-D(P*TP*GP*CP*AP*G)-3')
- EC
- 3.1.4.-
- UniProt
- Q5XJA0
- Ligands
- NA, MG
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 250 | 22% helix, 36% strand | Q5XJA0 |
| B | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 257 | 24% helix, 34% strand | Q5XJA0 |
| C | DNA (5'-D(P*TP*GP*CP*AP*G)-3') | dna | 5 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains B, A, C
- GOL · Glycerol · additive · 3 copies · chains A, B
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 | 1105 | 0.80 | 0.82 | 100 | GOL, MG |
| 2 | 76 | 0.31 | 0.74 | 19 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 701 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 571 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 187 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 4FPV · Crystal structure of D. rerio TDP2 complexed with single strand DNA product · the same entry in another collection · chain A against A, TM-score 1.00
- Q5XJA0 · AlphaFold monomer V2.0 prediction for tyrosyl-DNA phosphodiesterase 2 (Q5XJA0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q5XJA0
- Elsewhere: RCSB PDB 4FPV · PDBe 4FPV · UniProt Q5XJA0
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