Research workbench
Crystal structure of the complex of hujovi-1 Fab with the human A6 T- cell receptor TRBC1
Analyse Crystal structure of the complex of hujovi-1 Fab with the human A6 T- cell… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AMP
- Type
- protein
- Length
- 880 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha chain of A6 T-cell receptor; Beta chain 1 of A6 T-cell receptor TRBC1; Hujovi-1 Fab…
- Ligands
- ZN, CL
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha chain of A6 T-cell receptor | protein | 200 | 2% helix, 45% strand | — |
| B | Beta chain 1 of A6 T-cell receptor TRBC1 | protein | 243 | 7% helix, 47% strand | — |
| H | Hujovi-1 Fab heavy chain | protein | 220 | 6% helix, 49% strand | — |
| L | Hujovi-1 Fab light chain | protein | 217 | 5% helix, 49% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains H, L
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1149 | 0.71 | 0.75 | 94 | CL |
| 2 | 561 | 0.61 | 0.74 | 58 | empty |
| 3 | 218 | 0.56 | 0.79 | 22 | empty |
| 4 | 133 | 0.44 | 0.77 | 22 | empty |
| 5 | 131 | 0.44 | 0.76 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2240 Ų buried · 24 hydrogen bonds · protein-protein
- H–L · 1901 Ų buried · 17 hydrogen bonds · protein-protein
- B–H · 419 Ų buried · 12 hydrogen bonds · protein-protein
- B–L · 235 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 7AMP · Crystal structure of the complex of HuJovi-1 Fab with the human A6 T-cell receptor TRBC1 · the same entry in another collection · chain A against A, 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 7AMP · PDBe 7AMP
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