Research workbench
Crystal structure of the complex of the kfn mutant of hujovi-1 Fab with human TRBC2
Analyse Crystal structure of the complex of the kfn mutant of hujovi-1 Fab with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AMS
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human A6 T-cell receptor alpha chain; Human A6 T-cell receptor beta chain TRBC2; Human…
- Ligands
- ZN, CL
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human A6 T-cell receptor alpha chain | protein | 201 | 5% helix, 46% strand | — |
| B | Human A6 T-cell receptor beta chain TRBC2 | protein | 240 | 7% helix, 50% strand | — |
| H | Human jovi-1 Fab, kfn mutant, heavy chain | protein | 218 | 10% helix, 50% strand | — |
| L | Human jovi-1 Fab, kfn mutant, light chain | protein | 217 | 6% helix, 51% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains H, L
- CL · Chloride ion · ion · 2 copies · chains H, L
- GOL · Glycerol · additive · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.72 | 0.76 | 82 | empty |
| 2 | 684 | 0.64 | 0.74 | 65 | empty |
| 3 | 302 | 0.58 | 0.77 | 45 | empty |
| 4 | 238 | 0.54 | 0.77 | 33 | empty |
| 5 | 131 | 0.44 | 0.77 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2184 Ų buried · 23 hydrogen bonds · protein-protein
- H–L · 1801 Ų buried · 18 hydrogen bonds · protein-protein
- B–H · 457 Ų buried · 9 hydrogen bonds · protein-protein
- B–L · 235 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 7AMS · Crystal structure of the complex of the KFN mutant of HuJovi-1 Fab with human TRBC2 · the same entry in another collection · chain B against B, 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 7AMS · PDBe 7AMS
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