MolNFT v1 · #156211 · protein + DNA
Crystal structure of human NEIL1(R242, Y244R) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine
6LWP · Endonuclease 8-like 1: “Crystal structure of human NEIL1(R242, Y244R) bound to duplex DNA containing…”. X-ray diffraction, 15 pockets (best druggability 0.70). MolNFT v1 #156211 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6LWP
- Type
- protein + DNA
- Length
- 838 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease 8-like 1; DNA (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3'); DNA…
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- Q96FI4
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 28% 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 | 266 | 27% helix, 26% strand | Q96FI4 |
| B, E, H | DNA (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3') | dna | 13 | — | — |
| C, F, I | DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3') | dna | 13 | — | — |
| D | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 260 | 27% helix, 26% strand | Q96FI4 |
| G | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 234 | 30% helix, 22% strand | Q96FI4 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.70 | 0.78 | 48 | empty |
| 2 | 619 | 0.70 | 0.78 | 53 | GOL |
| 3 | 490 | 0.66 | 0.78 | 37 | empty |
| 4 | 430 | 0.63 | 0.77 | 37 | empty |
| 5 | 328 | 0.62 | 0.78 | 42 | empty |
Interfaces
15 interfaces between chains.
- D–E · 733 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 710 Ų buried · 22 hydrogen bonds · protein-nucleic
- G–H · 677 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–D · 580 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 534 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 6LWP · Crystal structure of human NEIL1(R242, Y244R) bound to duplex DNA containing… · the same entry in another collection · chain I against I, TM-score 1.00
- Q96FI4 · AlphaFold monomer V2.0 prediction for endonuclease 8-like 1 (Q96FI4) · a predicted model of the same protein · chain G against A, TM-score 0.99
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 6LWP · PDBe 6LWP · UniProt Q96FI4
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