Research workbench
Crystal structure of the burkholderia pseudomallei antitoxin hicb
Analyse Crystal structure of the burkholderia pseudomallei antitoxin hicb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G1N
- Type
- protein
- Length
- 534 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antitoxin hicb
- UniProt
- Q63NA5
- Ligands
- CL
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Antitoxin hicb | protein | 132 | 41% helix, 23% strand | Q63NA5 |
| C, D | Antitoxin hicb | protein | 135 | 38% helix, 25% strand | Q63NA5 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.71 | 0.77 | 68 | CL, GOL |
| 2 | 662 | 0.69 | 0.77 | 54 | CL, GOL |
| 3 | 56 | 0.35 | 0.78 | 11 | empty |
| 4 | 61 | 0.35 | 0.77 | 12 | empty |
| 5 | 97 | 0.34 | 0.74 | 16 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1911 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1897 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 872 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 859 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 227 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6G1N · Crystal structure of the Burkholderia Pseudomallei antitoxin HicB · 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 Q63NA5
- Elsewhere: RCSB PDB 6G1N · PDBe 6G1N · UniProt Q63NA5
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