Research workbench
Structure of 3' phosphatase nexo (D146N) from neisseria bound to product DNA hairpin
Analyse Structure of 3' phosphatase nexo (D146N) from neisseria bound to product DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FKE
- Type
- protein + DNA
- Length
- 269 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exodeoxyribonuclease III; DNA (5'-D(*GP*TP*AP*GP*CP*GP*AP*AP*GP*CP*TP*A)-3')
- EC
- 3.1.11.2
- UniProt
- Q9K100
- Ligands
- MN
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exodeoxyribonuclease III (EC 3.1.11.2) | protein | 257 | 31% helix, 26% strand | Q9K100 |
| B | DNA (5'-D(*GP*TP*AP*GP*CP*GP*AP*AP*GP*CP*TP*A)-3') | dna | 12 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.50 | 0.79 | 22 | empty |
| 2 | 70 | 0.33 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 745 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 6FKE · Structure of 3' phosphatase NExo (D146N) from Neisseria bound to product DNA hairpin · 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 Q9K100
- Elsewhere: RCSB PDB 6FKE · PDBe 6FKE · UniProt Q9K100
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