Research workbench
Substate bound inactive mutant of neisseria ap endonuclease in presence of metal ions
Analyse Substate bound inactive mutant of neisseria ap endonuclease in presence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B5H
- Type
- protein + DNA
- Length
- 281 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*3DRP*CP*AP*TP*CP*GP)-3'…
- EC
- 3.1.11.2
- UniProt
- C9X331
- Ligands
- MN
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative exodeoxyribonuclease (EC 3.1.11.2) | protein | 259 | 27% helix, 26% strand | C9X331 |
| U | 5'-D(*GP*CP*TP*AP*CP*3DRP*CP*AP*TP*CP*GP)-3' | dna | 11 | — | — |
| V | 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3' | dna | 11 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains A, U
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.51 | 0.85 | 16 | empty |
| 2 | 100 | 0.51 | 0.83 | 29 | empty |
| 3 | 95 | 0.38 | 0.77 | 14 | empty |
| 4 | 54 | 0.31 | 0.77 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–U · 773 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–V · 500 Ų buried · 16 hydrogen bonds · protein-nucleic
- U–V · 462 Ų buried · 34 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4B5H · Substate bound inactive mutant of Neisseria AP endonuclease in presence of metal ions · 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 4B5H · PDBe 4B5H · UniProt C9X331
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