Research workbench
Neisseria ap endonuclease bound to the substrate with an orphan adenine base
Analyse Neisseria ap endonuclease bound to the substrate with an orphan adenine base in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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