Research workbench
Crystal structure of a nigd-like immunity protein (BACCAC_03262) from bacteroides caccae atcc 43185 at 2.42 a resolution
Analyse Crystal structure of a nigd-like immunity protein (BACCAC_03262) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QWN
- Type
- protein
- Length
- 2,463 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical nigd-like protein
- UniProt
- A5ZK25
- Ligands
- CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 5% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Hypothetical nigd-like protein | protein | 206 | 5% helix, 55% strand | A5ZK25 |
| B | Hypothetical nigd-like protein | protein | 207 | 5% helix, 56% strand | A5ZK25 |
| C, L | Hypothetical nigd-like protein | protein | 203 | 5% helix, 57% strand | A5ZK25 |
| D | Hypothetical nigd-like protein | protein | 204 | 5% helix, 57% strand | A5ZK25 |
| E, F, I | Hypothetical nigd-like protein | protein | 205 | 5% helix, 57% strand | A5ZK25 |
| G | Hypothetical nigd-like protein | protein | 207 | 5% helix, 56% strand | A5ZK25 |
| J | Hypothetical nigd-like protein | protein | 208 | 5% helix, 56% strand | A5ZK25 |
| K | Hypothetical nigd-like protein | protein | 204 | 5% helix, 56% strand | A5ZK25 |
Ligands and binding sites
- CL · Chloride ion · ion · 41 copies · chains A, D, B, C, E, H, F, G, I, L, J, K
- EDO · 1,2-ethanediol · additive · 3 copies · chains D, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.79 | 0.86 | 56 | CL |
| 2 | 496 | 0.79 | 0.86 | 59 | CL |
| 3 | 565 | 0.78 | 0.84 | 50 | CL |
| 4 | 419 | 0.77 | 0.86 | 51 | CL |
| 5 | 459 | 0.76 | 0.84 | 44 | empty |
Interfaces
16 interfaces between chains.
- G–H · 998 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 907 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 897 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 871 Ų buried · 11 hydrogen bonds · protein-protein
- J–K · 861 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 3QWN · Crystal structure of a NigD-like immunity protein (BACCAC_03262) from Bacteroides caccae… · 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 A5ZK25
- Elsewhere: RCSB PDB 3QWN · PDBe 3QWN · UniProt A5ZK25
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