Research workbench
1.2 Angstrom Resolution Crystal Structure of Nucleoside Triphosphatase NudI from Klebsiella pneumoniae in Complex with HEPES
Analyse 1.2 Angstrom Resolution Crystal Structure of Nucleoside Triphosphatase NudI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DT3
- Type
- protein
- Length
- 287 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.2
- Source
- Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
- Molecule
- Nucleoside triphosphatase NudI
- EC
- 3.6.1.9, 3.6.1.12, 3.6.1.-, 3.6.1.23
- UniProt
- A0A1W1Q5B1
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.2 · 2 distinct chains · 20% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside triphosphatase NudI (EC 3.6.1.9, 3.6.1.12, 3.6.1.-, 3.6.1.23) | protein | 143 | 20% helix, 46% strand | A0A1W1Q5B1 |
| B | Nucleoside triphosphatase NudI (EC 3.6.1.9, 3.6.1.12, 3.6.1.-, 3.6.1.23) | protein | 144 | 19% helix, 45% strand | A0A1W1Q5B1 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.72 | 0.88 | 33 | EPE |
| 2 | 259 | 0.58 | 0.78 | 33 | empty |
| 3 | 178 | 0.53 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 928 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 6DT3 · 1.2 ångström resolution crystal structure of nucleoside triphosphatase nudi from… · 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 A0A1W1Q5B1
- Elsewhere: RCSB PDB 6DT3 · PDBe 6DT3 · UniProt A0A1W1Q5B1
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