MolNFT v1 · #122590 · protein + DNA
Crystal structure of human NEIL1(242K) bound to duplex DNA containing thf
5ITU · Endonuclease 8-like 1: “Crystal structure of human NEIL1(242K) bound to duplex DNA containing thf”. X-ray diffraction, 14 pockets (best druggability 0.74). MolNFT v1 #122590 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5ITU
- Type
- protein + DNA
- Length
- 872 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*CP*GP*TP*CP*TP*AP*C)-3'); DNA…
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- Q96FI4
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 27% 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 | 268 | 27% helix, 25% strand | Q96FI4 |
| B | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 255 | 27% helix, 27% strand | Q96FI4 |
| C | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 271 | 28% helix, 15% strand | Q96FI4 |
| D, F, H | DNA (5'-D(*CP*GP*TP*CP*CP*AP*CP*GP*TP*CP*TP*AP*C)-3') | dna | 13 | — | — |
| E, G, I | DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3') | dna | 13 | — | — |
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.74 | 0.77 | 49 | empty |
| 2 | 474 | 0.71 | 0.81 | 29 | empty |
| 3 | 535 | 0.67 | 0.78 | 51 | empty |
| 4 | 495 | 0.66 | 0.78 | 37 | empty |
| 5 | 563 | 0.66 | 0.77 | 42 | empty |
Interfaces
15 interfaces between chains.
- A–D · 665 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–F · 648 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–H · 600 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 594 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 527 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Compared structures
- 5ITU · Crystal Structure of Human NEIL1(242K) bound to duplex DNA containing THF · the same entry in another collection · chain H against H, TM-score 1.00
- Q96FI4 · AlphaFold monomer V2.0 prediction for endonuclease 8-like 1 (Q96FI4) · a predicted model of the same protein · chain B 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 5ITU · PDBe 5ITU · UniProt Q96FI4
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