Research workbench
Fab complex with grobeta. abvance: increasing our knowledge of antibody structural space to enable faster and better decision-making in antibody drug discovery.
Analyse Fab complex with grobeta. abvance: increasing our knowledge of antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OB5
- Type
- protein
- Length
- 496 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-X-C motif chemokine 2; Fab heavy chain; Fab light chain
- UniProt
- P19875
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-X-C motif chemokine 2 | protein | 63 | 22% helix, 30% strand | P19875 |
| H | Fab heavy chain | protein | 220 | 8% helix, 52% strand | — |
| L | Fab light chain | protein | 213 | 6% helix, 52% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains H, L
- GOL · Glycerol · additive · 4 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.61 | 0.74 | 56 | GOL |
| 2 | 60 | 0.57 | 0.90 | 21 | GOL |
| 3 | 88 | 0.41 | 0.78 | 17 | empty |
| 4 | 124 | 0.39 | 0.74 | 24 | GOL |
| 5 | 65 | 0.33 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1880 Ų buried · 21 hydrogen bonds · protein-protein
- A–H · 394 Ų buried · 3 hydrogen bonds · protein-protein
- A–L · 305 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5OB5 · fAb complex with GroBeta. AbVance: increasing our knowledge of antibody structural space… · the same entry in another collection · chain A against A, TM-score 1.00
- P19875 · AlphaFold monomer V2.0 prediction for C-X-C motif chemokine 2 (P19875) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P19875
- Elsewhere: RCSB PDB 5OB5 · PDBe 5OB5 · UniProt P19875
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