MolNFT v1 · #35394 · protein + DNA
Crystal structure of the DNA repair enzyme endonuclease-VIII (nei) from E. COLI in complex with ap-site containing DNA substrate
2EA0 · Endonuclease VIII: “Crystal structure of the DNA repair enzyme endonuclease-VIII (nei) from E. COLI in complex with ap-site…”. X-ray diffraction, 2 ligands (ZN, SO4), 3 pockets (best druggability 0.69). MolNFT v1 #35394 on…
- PDB
- 2EA0
- Type
- protein + DNA
- Length
- 278 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease VIII; 5'-D(P*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3'…
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- P50465
- Ligands
- ZN, SO4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease VIII (EC 3.2.2.-, 4.2.99.18) | protein | 254 | 31% helix, 24% strand | P50465 |
| B | 5'-D(P*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3' | dna | 12 | — | — |
| C | 5'-D(P*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3' | dna | 12 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A, C
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.69 | 0.82 | 40 | GOL, SO4 |
| 2 | 244 | 0.49 | 0.75 | 32 | empty |
| 3 | 113 | 0.44 | 0.78 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 613 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–C · 543 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- A–B · 484 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2EA0 · Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli in… · the same entry in another collection · chain A against A, TM-score 1.00
- P50465 · AlphaFold monomer V2.0 prediction for endonuclease 8 (P50465) · a predicted model of the same protein · chain A 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 P50465
- Elsewhere: RCSB PDB 2EA0 · PDBe 2EA0 · UniProt P50465
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