Research workbench
Crystal structure of human NEIL1(K242) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine
Analyse Crystal structure of human NEIL1(K242) 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
- 6LWM
- Type
- protein + DNA
- Length
- 825 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 0.72
Structure
x-ray diffraction · 5 distinct chains · 28% 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 | 27% helix, 27% 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 | 261 | 27% helix, 28% strand | Q96FI4 |
| G | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 221 | 31% helix, 18% 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.72 | 0.79 | 49 | empty |
| 2 | 663 | 0.70 | 0.78 | 62 | GOL |
| 3 | 449 | 0.65 | 0.78 | 41 | empty |
| 4 | 508 | 0.62 | 0.75 | 35 | empty |
| 5 | 301 | 0.61 | 0.79 | 47 | empty |
Interfaces
15 interfaces between chains.
- D–E · 717 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–B · 711 Ų buried · 18 hydrogen bonds · protein-nucleic
- G–H · 647 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–D · 613 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 531 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 6LWM · Crystal structure of human NEIL1(K242) 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 6LWM · PDBe 6LWM · UniProt Q96FI4
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