MolNFT v1 · #122587 · protein + DNA
Crystal structure of human NEIL1(P2G) bound to duplex DNA containing thf
5ITR · Endonuclease 8-like 1: “Crystal structure of human NEIL1(P2G) bound to duplex DNA containing thf”. X-ray diffraction, 12 pockets (best druggability 0.72). MolNFT v1 #122587 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5ITR
- Type
- protein + DNA
- Length
- 863 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 0.72
Structure
x-ray diffraction · 5 distinct chains · 25% 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 | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 261 | 23% helix, 27% strand | Q96FI4 |
| C | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 254 | 24% helix, 17% strand | Q96FI4 |
| D, E | DNA (26-mer) | dna | 26 | — | — |
| F | DNA (26-mer) | dna | 26 | — | — |
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 | 682 | 0.72 | 0.79 | 43 | empty |
| 2 | 787 | 0.71 | 0.77 | 69 | empty |
| 3 | 618 | 0.67 | 0.77 | 42 | empty |
| 4 | 686 | 0.64 | 0.74 | 37 | empty |
| 5 | 466 | 0.63 | 0.77 | 38 | empty |
Interfaces
7 interfaces between chains.
- B–E · 1000 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–D · 989 Ų buried · 30 hydrogen bonds · protein-nucleic
- C–F · 913 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 591 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 466 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5ITR · Crystal Structure of Human NEIL1(P2G) bound to duplex DNA containing THF · the same entry in another collection · chain B against B, 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 0.98
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 5ITR · PDBe 5ITR · UniProt Q96FI4
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