MolNFT v1 · #156204 · protein + DNA
Crystal structure of human NEIL1(P2G, E3Q, R242) bound to duplex DNA containing dihydrothymine (dht)
6LWI · Endonuclease 8-like 1: “Crystal structure of human NEIL1(P2G, E3Q, R242) bound to duplex DNA containing dihydrothymine (dht)”. X-ray diffraction, 15 pockets (best druggability 0.74). MolNFT v1 #156204 on GenesisL1: 3D structure…
- PDB
- 6LWI
- Type
- protein + DNA
- Length
- 842 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*(TDH)P*GP*TP*CP*TP*AP*C)-3'); DNA…
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- Q96FI4
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 28% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 269 | 27% helix, 25% strand | Q96FI4 |
| B, E, H | DNA (5'-D(*CP*GP*TP*CP*CP*AP*(TDH)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 | 270 | 27% helix, 25% strand | Q96FI4 |
| G | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 225 | 31% helix, 15% strand | Q96FI4 |
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 | 535 | 0.74 | 0.82 | 32 | empty |
| 2 | 494 | 0.67 | 0.79 | 40 | empty |
| 3 | 551 | 0.64 | 0.76 | 62 | empty |
| 4 | 471 | 0.63 | 0.77 | 40 | empty |
| 5 | 501 | 0.62 | 0.76 | 36 | empty |
Interfaces
15 interfaces between chains.
- A–B · 759 Ų buried · 22 hydrogen bonds · protein-nucleic
- D–E · 740 Ų buried · 20 hydrogen bonds · protein-nucleic
- G–H · 659 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–D · 633 Ų buried · 10 hydrogen bonds · protein-protein
- H–I · 531 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 6LWI · 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 0.98
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 6LWI · PDBe 6LWI · UniProt Q96FI4
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