MolNFT v1 · #122593 · protein + DNA
Crystal structure of human NEIL1(P2G R242K) bound to duplex DNA containing thymine glycol
5ITX · Endonuclease 8-like 1: “Crystal structure of human NEIL1(P2G R242K) bound to duplex DNA containing thymine glycol”. X-ray diffraction, 13 pockets (best druggability 0.72). MolNFT v1 #122593 on GenesisL1: 3D structure, binding sites…
- PDB
- 5ITX
- Type
- protein + DNA
- Length
- 865 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease 8-like 1; DNA (26-mer)
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- Q96FI4
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 264 | 27% helix, 28% strand | Q96FI4 |
| D, C, F | DNA (26-mer) | dna | 26 | — | — |
| B | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 263 | 25% helix, 25% strand | Q96FI4 |
| E | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 260 | 25% helix, 20% strand | Q96FI4 |
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.72 | 0.79 | 45 | empty |
| 2 | 688 | 0.71 | 0.78 | 62 | empty |
| 3 | 641 | 0.67 | 0.76 | 38 | empty |
| 4 | 506 | 0.66 | 0.78 | 37 | empty |
| 5 | 487 | 0.65 | 0.77 | 37 | empty |
Interfaces
7 interfaces between chains.
- A–D · 1097 Ų buried · 30 hydrogen bonds · protein-nucleic
- B–C · 1053 Ų buried · 31 hydrogen bonds · protein-nucleic
- E–F · 1037 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–B · 581 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 438 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 5ITX · Crystal Structure of Human NEIL1(P2G R242K) bound to duplex DNA containing Thymine Glycol · the same entry in another collection · chain F against F, TM-score 1.00
- Q96FI4 · AlphaFold monomer V2.0 prediction for endonuclease 8-like 1 (Q96FI4) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q96FI4
- Elsewhere: RCSB PDB 5ITX · PDBe 5ITX · UniProt Q96FI4
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