Research workbench
Crystal structure of human NEIL1(P2G R242K) bound to duplex DNA containing thymine glycol
Analyse Crystal structure of human NEIL1(P2G R242K) bound to duplex DNA containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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