Research workbench
Crystal structure of SAG173-04
Analyse Crystal structure of SAG173-04 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DUR
- Type
- protein
- Length
- 466 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody fv fragment SAG173-04; Ig-like protein
- Ligands
- KDO, MG
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Antibody fv fragment SAG173-04 | protein | 112 | 3% helix, 54% strand | — |
| B, D | Ig-like protein | protein | 121 | 7% helix, 49% 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 · 2 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 | 497 | 0.67 | 0.78 | 45 | MG |
| 2 | 264 | 0.57 | 0.78 | 40 | KDO, PG4 |
| 3 | 84 | 0.31 | 0.73 | 19 | empty |
| 4 | 75 | 0.30 | 0.73 | 20 | empty |
| 5 | 54 | 0.28 | 0.75 | 15 | empty |
Interfaces
5 interfaces between chains.
- C–D · 886 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 873 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 239 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 226 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3DUR · Crystal structure of SAG173-04 · 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 3DUR · PDBe 3DUR
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