MolNFT v1 · #122594 · protein + DNA
Crystal structure of human NEIL1(P2G) bound to duplex DNA containing thymine glycol
5ITY · Endonuclease 8-like 1: “Crystal structure of human NEIL1(P2G) bound to duplex DNA containing thymine glycol”. X-ray diffraction, 14 pockets (best druggability 0.72). MolNFT v1 #122594 on GenesisL1: 3D structure, binding sites and…
- 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
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