MolNFT v1 · #156213 · protein + DNA
Crystal structure of human NEIL1(K242) bound to duplex DNA containing a cleaved C:T mismatch
6LWR · Endonuclease 8-like 1: “Crystal structure of human NEIL1(K242) bound to duplex DNA containing a cleaved C:T mismatch”. X-ray diffraction, 1 ligand (AD2), 5 pockets (best druggability 0.72). MolNFT v1 #156213 on GenesisL1: 3D…
- PDB
- 6LWR
- Type
- protein + DNA
- Length
- 578 residues
- Chains
- 8
- 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*(PDA))-3'); DNA…
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- Q96FI4
- Ligands
- AD2
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 270 | 28% helix, 26% strand | Q96FI4 |
| B, F | DNA (5'-D(*CP*GP*TP*CP*CP*(PDA))-3') | dna | 5 | — | — |
| C, G | DNA (5'-D(*CP*GP*TP*CP*CP*(PDA))-3') | dna | 6 | — | — |
| D, H | DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3') | dna | 13 | — | — |
| E | Endonuclease 8-like 1 (EC 3.2.2.-, 4.2.99.18) | protein | 260 | 30% helix, 26% strand | Q96FI4 |
Ligands and binding sites
- AD2 · 2'-deoxy-adenosine-3'-5'-diphosphate · ligand · 2 copies · chains A, B, D, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.72 | 0.76 | 69 | AD2 |
| 2 | 551 | 0.67 | 0.78 | 46 | empty |
| 3 | 768 | 0.66 | 0.74 | 65 | AD2 |
| 4 | 313 | 0.55 | 0.75 | 25 | empty |
| 5 | 117 | 0.38 | 0.75 | 21 | empty |
Interfaces
9 interfaces between chains.
- A–E · 590 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 415 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 394 Ų buried · 11 hydrogen bonds · protein-nucleic
- E–H · 362 Ų buried · 8 hydrogen bonds · protein-nucleic
- E–G · 357 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6LWR · Crystal structure of human NEIL1(K242) bound to duplex DNA containing a cleaved C:T… · 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 E 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 6LWR · PDBe 6LWR · UniProt Q96FI4
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