MolNFT v1 · #156872 · protein
Structure of the human 4-1BB / urelumab Fab complex
6MHR · Urelumab Fab heavy chain: “Structure of the human 4-1BB / urelumab Fab complex”. X-ray diffraction, 3 ligands (NAG, FUC, BMA), 10 pockets (best druggability 0.62). MolNFT v1 #156872 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6MHR
- Type
- protein
- Length
- 1,147 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urelumab Fab heavy chain; Urelumab Fab kappa chain; Tumor necrosis factor receptor…
- UniProt
- Q07011
- Ligands
- NAG, FUC, BMA
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Urelumab Fab heavy chain | protein | 217 | 6% helix, 53% strand | — |
| E, B | Urelumab Fab kappa chain | protein | 215 | 7% helix, 52% strand | — |
| A | Urelumab Fab heavy chain | protein | 219 | 3% helix, 53% strand | — |
| F | Tumor necrosis factor receptor superfamily member 9 | protein | 140 | 6% helix, 31% strand | Q07011 |
| C | Tumor necrosis factor receptor superfamily member 9 | protein | 141 | 5% helix, 31% strand | Q07011 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains F, C
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains F, C
- BMA · beta-D-mannopyranose · sugar
- MLI · Malonate ion · additive · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains F, C
- GOL · Glycerol · additive · chains D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.62 | 0.75 | 71 | empty |
| 2 | 372 | 0.56 | 0.74 | 54 | empty |
| 3 | 54 | 0.48 | 0.86 | 21 | empty |
| 4 | 71 | 0.43 | 0.81 | 21 | empty |
| 5 | 152 | 0.42 | 0.74 | 28 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1824 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1740 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 510 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 478 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 385 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6MHR · Structure of the human 4-1BB / Urelumab 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 C against A, TM-score 0.64
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 6MHR · PDBe 6MHR · UniProt Q07011
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