Research workbench
Crystal structure of nucleotidyltransferase-like protein (ZP_00538802.1) from exiguobacterium sibiricum 255-15 at 1.90 a resolution
Analyse Crystal structure of nucleotidyltransferase-like protein (ZP_00538802.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C18
- Type
- protein
- Length
- 869 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleotidyltransferase-like protein
- UniProt
- Q41F96
- Ligands
- CL
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nucleotidyltransferase-like protein | protein | 290 | 58% helix, 19% strand | Q41F96 |
| B | Nucleotidyltransferase-like protein | protein | 289 | 58% helix, 19% strand | Q41F96 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.81 | 0.82 | 117 | GOL |
| 2 | 356 | 0.65 | 0.80 | 46 | GOL |
| 3 | 101 | 0.44 | 0.78 | 19 | empty |
| 4 | 104 | 0.41 | 0.77 | 23 | empty |
| 5 | 84 | 0.41 | 0.78 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2575 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 385 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 333 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3C18 · Crystal structure of nucleotidyltransferase-like protein (ZP_00538802.1) 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 Q41F96
- Elsewhere: RCSB PDB 3C18 · PDBe 3C18 · UniProt Q41F96
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