MolNFT v1 · #156200 · protein + DNA
Crystal structure of human NEIL1(P2G, E3Q, R242) bound to duplex DNA containing spiroiminodihydantoin (sp)
6LWD · Endonuclease 8-like 1: “Crystal structure of human NEIL1(P2G, E3Q, R242) bound to duplex DNA containing spiroiminodihydantoin (sp)”. X-ray diffraction, 15 pockets (best druggability 0.72). MolNFT v1 #156200 on GenesisL1: 3D…
- 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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