Research workbench
Crystal structure of human NEIL1(P2G) bound to duplex DNA containing thymine glycol
Analyse Crystal structure of human NEIL1(P2G) bound to duplex DNA containing thymine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ITY
- Type
- protein + DNA
- Length
- 866 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
- 14 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 265 | 26% helix, 26% strand | Q96FI4 |
| B | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 262 | 26% helix, 26% strand | Q96FI4 |
| C | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 261 | 28% helix, 21% strand | Q96FI4 |
| D, E, F | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.72 | 0.77 | 75 | GOL |
| 2 | 501 | 0.71 | 0.81 | 33 | empty |
| 3 | 495 | 0.67 | 0.79 | 35 | empty |
| 4 | 374 | 0.66 | 0.80 | 26 | empty |
| 5 | 558 | 0.64 | 0.76 | 35 | empty |
Interfaces
7 interfaces between chains.
- C–F · 1117 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–D · 1091 Ų buried · 33 hydrogen bonds · protein-nucleic
- B–E · 1060 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–B · 594 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 444 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 5ITY · Crystal Structure of Human NEIL1(P2G) 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 5ITY · PDBe 5ITY · UniProt Q96FI4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.