Research workbench
Structure of TIPC2 from streptococcus intermedius B196
Analyse Structure of TIPC2 from streptococcus intermedius B196 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DHX
- Type
- protein
- Length
- 539 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TIPC2
- UniProt
- T1ZH71
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TIPC2 | protein | 182 | 30% helix, 38% strand | T1ZH71 |
| B | TIPC2 | protein | 180 | 29% helix, 38% strand | T1ZH71 |
| C | TIPC2 | protein | 177 | 28% helix, 39% strand | T1ZH71 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.60 | 0.76 | 45 | empty |
| 2 | 118 | 0.39 | 0.75 | 22 | SO4 |
| 3 | 58 | 0.34 | 0.78 | 12 | empty |
| 4 | 50 | 0.31 | 0.77 | 15 | empty |
| 5 | 54 | 0.29 | 0.75 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–C · 673 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 400 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (engineered).
Compared structures
- 6DHX · Structure of TipC2 from Streptococcus intermedius B196 · 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 T1ZH71
- Elsewhere: RCSB PDB 6DHX · PDBe 6DHX · UniProt T1ZH71
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