Research workbench
Crystal structure of Fab in complex with mouse CD96 monomer
Analyse Crystal structure of Fab in complex with mouse CD96 monomer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S11
- Type
- protein
- Length
- 2,141 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface protein tactile; Fab heavy chain; Fab light chain
- UniProt
- Q3U0X8
- Ligands
- NAG, SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 10 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | T-cell surface protein tactile | protein | 113 | 5% helix, 58% strand | Q3U0X8 |
| H, K | Fab heavy chain | protein | 218 | 6% helix, 50% strand | — |
| L | Fab light chain | protein | 212 | 7% helix, 54% strand | — |
| I | Fab heavy chain | protein | 214 | 7% helix, 50% strand | — |
| M | Fab light chain | protein | 211 | 8% helix, 55% strand | — |
| E | T-cell surface protein tactile | protein | 95 | 6% helix, 43% strand | Q3U0X8 |
| J | Fab heavy chain | protein | 219 | 7% helix, 50% strand | — |
| N | Fab light chain | protein | 215 | 7% helix, 53% strand | — |
| F | T-cell surface protein tactile | protein | 102 | 6% helix, 49% strand | Q3U0X8 |
| O | Fab light chain | protein | 211 | 8% helix, 57% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C, D
- SO4 · Sulfate ion · ion · 6 copies · chains C, L, D, N, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.74 | 0.79 | 79 | empty |
| 2 | 1125 | 0.71 | 0.76 | 125 | empty |
| 3 | 601 | 0.70 | 0.78 | 63 | empty |
| 4 | 596 | 0.65 | 0.76 | 66 | empty |
| 5 | 586 | 0.63 | 0.75 | 63 | empty |
Interfaces
20 interfaces between chains.
- J–N · 2156 Ų buried · 10 hydrogen bonds · protein-protein
- H–L · 2074 Ų buried · 6 hydrogen bonds · protein-protein
- K–O · 2020 Ų buried · 11 hydrogen bonds · protein-protein
- I–M · 1869 Ų buried · 6 hydrogen bonds · protein-protein
- E–J · 564 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 4 modified, 2 glycan (disulfide, cyclization, N-glycosylation).
Compared structures
- 7S11 · Crystal structure of Fab in complex with mouse CD96 monomer · the same entry in another collection · chain O against O, 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
- Every structure of UniProt Q3U0X8
- Elsewhere: RCSB PDB 7S11 · PDBe 7S11 · UniProt Q3U0X8
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