Research workbench
Crystal structure of SAG506-01, tetragonal, crystal 1
Analyse Crystal structure of SAG506-01, tetragonal, crystal 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DV4
- Type
- protein
- Length
- 231 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody fv fragment SAG506-01; Ig-like protein
- Ligands
- KDO, MG
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody fv fragment SAG506-01 | protein | 112 | 3% helix, 52% strand | — |
| B | Ig-like protein | protein | 119 | 3% helix, 50% strand | — |
Ligands and binding sites
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · chains A, B
- MG · Magnesium ion · metal · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.56 | 0.90 | 18 | empty |
| 2 | 88 | 0.32 | 0.73 | 22 | empty |
| 3 | 74 | 0.32 | 0.74 | 16 | KDO |
| 4 | 64 | 0.26 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 825 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3DV4 · Crystal structure of SAG506-01, tetragonal, crystal 1 · 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 3DV4 · PDBe 3DV4
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