MolNFT v1 · #144972 · protein
Crystal structure of humanized D. rerio TDP2 by 14 mutations
6CA4 · Tyrosyl-DNA phosphodiesterase 2: “Crystal structure of humanized D. rerio TDP2 by 14 mutations”. X-ray diffraction, 1 ligand (MG), 5 pockets (best druggability 0.80). MolNFT v1 #144972 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6CA4
- Type
- protein
- Length
- 716 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-DNA phosphodiesterase 2
- EC
- 3.1.4.-
- UniProt
- Q5XJA0
- Ligands
- MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 243 | 23% helix, 37% strand | Q5XJA0 |
| B | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 244 | 23% helix, 36% strand | Q5XJA0 |
| C | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 229 | 25% helix, 38% strand | Q5XJA0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C
- MLI · Malonate ion · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.80 | 0.81 | 89 | EDO, MG |
| 2 | 205 | 0.62 | 0.82 | 25 | EDO |
| 3 | 182 | 0.59 | 0.82 | 27 | empty |
| 4 | 125 | 0.55 | 0.82 | 22 | EDO, MLI |
| 5 | 89 | 0.37 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 575 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 519 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 153 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6CA4 · Crystal structure of humanized D. rerio TDP2 by 14 mutations · 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 B 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 6CA4 · PDBe 6CA4 · UniProt Q5XJA0
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