Research workbench
Crystal structure of the pts cellobiose specific enzyme iia from bacillus anthracis
Analyse Crystal structure of the pts cellobiose specific enzyme iia from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K1S
- Type
- protein
- Length
- 951 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pts system, cellobiose-specific iia component
- UniProt
- Q81X08
- Ligands
- NA, MG, CL
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Pts system, cellobiose-specific iia component | protein | 109 | 81% helix, 0% strand | Q81X08 |
| B, C, F, I | Pts system, cellobiose-specific iia component | protein | 104 | 88% helix, 0% strand | Q81X08 |
| E, G | Pts system, cellobiose-specific iia component | protein | 106 | 79% helix, 0% strand | Q81X08 |
| H | Pts system, cellobiose-specific iia component | protein | 105 | 81% helix, 0% strand | Q81X08 |
Ligands and binding sites
- NA · Sodium ion · metal · 14 copies · chains A, C, E, B, D, F, G, I, H
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D, E, F, G, H, I
- CL · Chloride ion · ion · 3 copies · chains B, C, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.80 | 0.81 | 77 | empty |
| 2 | 600 | 0.73 | 0.80 | 49 | CL |
| 3 | 483 | 0.72 | 0.81 | 61 | empty |
| 4 | 220 | 0.55 | 0.78 | 34 | empty |
| 5 | 179 | 0.53 | 0.78 | 27 | empty |
Interfaces
16 interfaces between chains.
- A–C · 1138 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1095 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 1082 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1081 Ų buried · 14 hydrogen bonds · protein-protein
- G–I · 1070 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 modified (engineered).
Compared structures
- 3K1S · Crystal Structure of the PTS Cellobiose Specific Enzyme IIA from Bacillus anthracis · 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 Q81X08
- Elsewhere: RCSB PDB 3K1S · PDBe 3K1S · UniProt Q81X08
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