Research workbench
Crystal structure of SAG506-01, orthorhombic, twinned, crystal 2
Analyse Crystal structure of SAG506-01, orthorhombic, twinned, crystal 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DUU
- Type
- protein
- Length
- 466 residues
- Chains
- 4
- 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
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Antibody fv fragment SAG506-01 | protein | 112 | 3% helix, 52% strand | — |
| B, D | Ig-like protein | protein | 121 | 2% helix, 50% strand | — |
Ligands and binding sites
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.68 | 0.79 | 44 | MG |
| 2 | 241 | 0.55 | 0.77 | 39 | KDO, PG4 |
| 3 | 87 | 0.33 | 0.74 | 18 | empty |
| 4 | 77 | 0.31 | 0.74 | 20 | empty |
| 5 | 63 | 0.30 | 0.75 | 14 | empty |
Interfaces
5 interfaces between chains.
- C–D · 861 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 841 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 245 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 199 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 84 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3DUU · Crystal structure of SAG506-01, orthorhombic, twinned, crystal 2 · 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 3DUU · PDBe 3DUU
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.