MolNFT v1 · #86398 · protein + DNA
Substate bound inactive mutant of neisseria ap endonuclease in presence of metal ions
4B5H · Putative exodeoxyribonuclease: “Substate bound inactive mutant of neisseria ap endonuclease in presence of metal ions”. X-ray diffraction, 1 ligand (MN), 4 pockets (best druggability 0.51). MolNFT v1 #86398 on GenesisL1: 3D…
- 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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