Research workbench
Crystal structure of human NEIL1(P2G, E3Q, R242) bound to duplex DNA containing spiroiminodihydantoin (sp)
Analyse Crystal structure of human NEIL1(P2G, E3Q, R242) 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
- 6LWD
- 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*(DSP)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, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 270 | 27% helix, 25% strand | Q96FI4 |
| B, E, H | DNA (5'-D(*CP*GP*TP*CP*CP*AP*(DSP)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 | 264 | 27% helix, 25% strand | Q96FI4 |
| G | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 226 | 31% helix, 19% 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.72 | 0.79 | 44 | empty |
| 2 | 527 | 0.65 | 0.77 | 55 | GOL |
| 3 | 477 | 0.65 | 0.77 | 38 | empty |
| 4 | 282 | 0.61 | 0.80 | 27 | empty |
| 5 | 391 | 0.59 | 0.76 | 38 | empty |
Interfaces
15 interfaces between chains.
- D–E · 733 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–B · 721 Ų buried · 24 hydrogen bonds · protein-nucleic
- G–H · 642 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–D · 601 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 531 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 6LWD · Crystal structure of human NEIL1(P2G, E3Q, R242) 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 6LWD · PDBe 6LWD · UniProt Q96FI4
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