Research workbench
Structure of the human 4-1BB / utomilumab Fab complex
Analyse Structure of the human 4-1BB / utomilumab Fab complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MI2
- Type
- protein
- Length
- 1,115 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Utomilumab Fab heavy chain; Utomilumab Fab lambda chain; Tumor necrosis factor receptor…
- UniProt
- Q07011
- Ligands
- NAG, FUC, SO4
- Pockets
- 17 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Utomilumab Fab heavy chain | protein | 209 | 3% helix, 46% strand | — |
| B, E | Utomilumab Fab lambda chain | protein | 210 | 7% helix, 50% strand | — |
| D | Utomilumab Fab heavy chain | protein | 210 | 4% helix, 50% strand | — |
| F | Tumor necrosis factor receptor superfamily member 9 | protein | 133 | 0% helix, 33% strand | Q07011 |
| C | Tumor necrosis factor receptor superfamily member 9 | protein | 143 | 8% helix, 31% strand | Q07011 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains F, C
- FUC · alpha-L-fucopyranose · sugar
- SO4 · Sulfate ion · ion · 20 copies · chains A, C, B, D, F, E
- GOL · Glycerol · additive · 9 copies · chains A, B, E, F, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.70 | 0.97 | 19 | empty |
| 2 | 56 | 0.65 | 0.95 | 20 | empty |
| 3 | 578 | 0.62 | 0.74 | 58 | GOL |
| 4 | 88 | 0.55 | 0.85 | 19 | empty |
| 5 | 115 | 0.53 | 0.82 | 19 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1532 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 1503 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 641 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 632 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 489 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6MI2 · Structure of the human 4-1BB / Utomilumab Fab complex · the same entry in another collection · chain C against C, TM-score 1.00
- Q07011 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member 9… · a predicted model of the same protein · chain F against A, TM-score 0.68
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 Q07011
- Elsewhere: RCSB PDB 6MI2 · PDBe 6MI2 · UniProt Q07011
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