MolNFT v1 · #92042 · protein
Crystal structure of truncated caenorhabditis elegans TDP2
4FVA · 5'-tyrosyl-DNA phosphodiesterase: “Crystal structure of truncated caenorhabditis elegans TDP2”. X-ray diffraction, 1 ligand (MG), 10 pockets (best druggability 0.77). MolNFT v1 #92042 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4FVA
- Type
- protein
- Length
- 998 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-tyrosyl-DNA phosphodiesterase
- EC
- 3.1.4.-
- UniProt
- Q9XWG3
- Ligands
- MG
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-tyrosyl-DNA phosphodiesterase (EC 3.1.4.-) | protein | 249 | 23% helix, 35% strand | Q9XWG3 |
| B | 5'-tyrosyl-DNA phosphodiesterase (EC 3.1.4.-) | protein | 250 | 23% helix, 35% strand | Q9XWG3 |
| C | 5'-tyrosyl-DNA phosphodiesterase (EC 3.1.4.-) | protein | 251 | 23% helix, 35% strand | Q9XWG3 |
| D | 5'-tyrosyl-DNA phosphodiesterase (EC 3.1.4.-) | protein | 248 | 23% helix, 35% strand | Q9XWG3 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C, D
- MLI · Malonate ion · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.77 | 0.86 | 44 | EDO |
| 2 | 393 | 0.75 | 0.85 | 48 | MLI |
| 3 | 313 | 0.54 | 0.75 | 34 | EDO |
| 4 | 110 | 0.40 | 0.75 | 18 | MG, MLI, EDO |
| 5 | 111 | 0.40 | 0.76 | 23 | MG, MLI, EDO |
Interfaces
5 interfaces between chains.
- B–C · 616 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 538 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 207 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 104 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 100 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4FVA · Crystal structure of truncated Caenorhabditis elegans TDP2 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9XWG3 · AlphaFold monomer V2.0 prediction for 5'-tyrosyl-DNA phosphodiesterase (Q9XWG3) · 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 Q9XWG3
- Elsewhere: RCSB PDB 4FVA · PDBe 4FVA · UniProt Q9XWG3
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