Research workbench
Crystal structure of antibody 438-B11 dss mutant (CYS98A-CYS100AA)
Analyse Crystal structure of antibody 438-B11 dss mutant (CYS98A-CYS100AA) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UUM
- Type
- protein
- Length
- 884 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B11 Fab light chain; B11 dss Fab heavy chain
- Ligands
- NAG, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, A | B11 Fab light chain | protein | 215 | 7% helix, 53% strand | — |
| H | B11 dss Fab heavy chain | protein | 227 | 9% helix, 49% strand | — |
| B | B11 dss Fab heavy chain | protein | 227 | 8% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains F, A
- SO4 · Sulfate ion · ion · 14 copies · chains F, H, B, A
- PG4 · Tetraethylene glycol · additive · 13 copies · chains F, H, A, B
- ACT · Acetate ion · additive · 2 copies
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 | 744 | 0.78 | 0.82 | 96 | PG4, SO4 |
| 2 | 177 | 0.53 | 0.79 | 39 | PG4 |
| 3 | 75 | 0.47 | 0.83 | 22 | SO4 |
| 4 | 139 | 0.44 | 0.76 | 24 | empty |
| 5 | 82 | 0.41 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2103 Ų buried · 15 hydrogen bonds · protein-protein
- F–H · 2068 Ų buried · 16 hydrogen bonds · protein-protein
- H–B · 527 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan, 1 covalent (disulfide, N-glycosylation, additive adduct).
Compared structures
- 6UUM · Crystal structure of antibody 438-B11 DSS mutant (Cys98A-Cys100aA) · the same entry in another collection · chain F against F, 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 6UUM · PDBe 6UUM
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