MolNFT v1 · #86400 · protein + DNA
Neisseria ap endonuclease bound to the substrate with an orphan adenine base
4B5J · Putative exodeoxyribonuclease: “Neisseria ap endonuclease bound to the substrate with an orphan adenine base”. X-ray diffraction, 3 pockets (best druggability 0.63). MolNFT v1 #86400 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4B5J
- Type
- protein + DNA
- Length
- 278 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative exodeoxyribonuclease; 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3'…
- EC
- 3.1.11.2
- UniProt
- C9X331
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative exodeoxyribonuclease (EC 3.1.11.2) | protein | 256 | 30% helix, 27% strand | C9X331 |
| U | 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3' | dna | 11 | — | — |
| V | 5'-D(*CP*GP*AP*TP*GP*AP*GP*TP*AP*GP*CP)-3' | dna | 11 | — | — |
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 | 107 | 0.63 | 0.89 | 26 | empty |
| 2 | 64 | 0.31 | 0.76 | 13 | empty |
| 3 | 65 | 0.31 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–U · 769 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–V · 534 Ų buried · 9 hydrogen bonds · protein-nucleic
- U–V · 479 Ų buried · 42 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4B5J · Neisseria AP endonuclease bound to the substrate with an orphan Adenine base · the same entry in another collection · chain A against A, TM-score 1.00
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 C9X331
- Elsewhere: RCSB PDB 4B5J · PDBe 4B5J · UniProt C9X331
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