MolNFT v1 · #173049 · protein
Crystal structure of the complex of the kfn mutant of jovi-1 Fab with human TRBC1
7AMR · Human T-cell receptor alpha chain: “Crystal structure of the complex of the kfn mutant of jovi-1 Fab with human TRBC1”. X-ray diffraction, 2 ligands (ZN, CL), 11 pockets (best druggability 0.72). MolNFT v1 #173049 on GenesisL1: 3D…
- PDB
- 7AMR
- Type
- protein
- Length
- 880 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human T-cell receptor alpha chain; Human T-cell receptor beta chain TRBC2; Human jovi-1…
- Ligands
- ZN, CL
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human T-cell receptor alpha chain | protein | 201 | 3% helix, 46% strand | — |
| B | Human T-cell receptor beta chain TRBC2 | protein | 240 | 8% helix, 50% strand | — |
| H | Human jovi-1 Fab fragment, kfn mutant, heavy chain | protein | 222 | 12% helix, 53% strand | — |
| L | Human jovi-1 Fab fragment, kfn mutant, light chain | protein | 217 | 5% 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 · 3 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.72 | 0.76 | 92 | empty |
| 2 | 651 | 0.63 | 0.74 | 60 | empty |
| 3 | 250 | 0.55 | 0.77 | 36 | empty |
| 4 | 218 | 0.55 | 0.78 | 28 | empty |
| 5 | 185 | 0.52 | 0.78 | 33 | CL |
Interfaces
4 interfaces between chains.
- A–B · 2132 Ų buried · 21 hydrogen bonds · protein-protein
- H–L · 1889 Ų buried · 18 hydrogen bonds · protein-protein
- B–H · 466 Ų buried · 7 hydrogen bonds · protein-protein
- B–L · 240 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 7AMR · Crystal structure of the complex of the KFN mutant of Jovi-1 Fab with human 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 7AMR · PDBe 7AMR
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