MolNFT v1 · #122589 · protein + DNA
Crystal structure of human NEIL1 bound to duplex DNA containing thf
5ITT · Endonuclease 8-like 1: “Crystal structure of human NEIL1 bound to duplex DNA containing thf”. X-ray diffraction, 12 pockets (best druggability 0.71). MolNFT v1 #122589 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ITT
- Type
- protein + DNA
- Length
- 869 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease 8-like 1; DNA (26-mer)
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- Q96FI4
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 271 | 27% helix, 25% strand | Q96FI4 |
| B | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 261 | 25% helix, 24% strand | Q96FI4 |
| C | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 259 | 25% helix, 26% strand | Q96FI4 |
| D, F | DNA (26-mer) | dna | 26 | — | — |
| E | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.71 | 0.76 | 77 | GOL |
| 2 | 685 | 0.70 | 0.78 | 41 | empty |
| 3 | 575 | 0.69 | 0.78 | 41 | GOL |
| 4 | 726 | 0.67 | 0.75 | 38 | empty |
| 5 | 441 | 0.65 | 0.79 | 38 | empty |
Interfaces
7 interfaces between chains.
- B–E · 1011 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–D · 983 Ų buried · 25 hydrogen bonds · protein-nucleic
- C–F · 937 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–B · 566 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 411 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5ITT · Crystal Structure of Human NEIL1 bound to duplex DNA containing THF · the same entry in another collection · chain F against F, TM-score 1.00
- Q96FI4 · AlphaFold monomer V2.0 prediction for endonuclease 8-like 1 (Q96FI4) · a predicted model of the same protein · chain C 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 5ITT · PDBe 5ITT · UniProt Q96FI4
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