Research workbench
Structure of S67-27 in complex with tsbp
Analyse Structure of S67-27 in complex with tsbp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IJS
- Type
- protein
- Length
- 875 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin light chain (IGG3); Immunoglobulin heavy chain (IGG3)
- Ligands
- GP4, KDO, MG
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin light chain (IGG3) | protein | 217 | 6% helix, 53% strand | — |
| B, D | Immunoglobulin heavy chain (IGG3) | protein | 221 | 7% helix, 49% strand | — |
| C | Immunoglobulin light chain (IGG3) | protein | 216 | 6% helix, 53% strand | — |
Ligands and binding sites
- GP4 · 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose · ligand · 2 copies · chains A, C
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 4 copies · chains B, A, D, C
- MG · Magnesium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.67 | 0.82 | 56 | empty |
| 2 | 766 | 0.67 | 0.75 | 69 | empty |
| 3 | 638 | 0.64 | 0.75 | 68 | empty |
| 4 | 391 | 0.62 | 0.77 | 44 | empty |
| 5 | 118 | 0.53 | 0.82 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1843 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1795 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 390 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 196 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 143 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3IJS · Structure of S67-27 in Complex with TSBP · 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
- Elsewhere: RCSB PDB 3IJS · PDBe 3IJS
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