Research workbench
Crystal structure of human CD81 large extracellular loop in complex with 5A6 Fab
Analyse Crystal structure of human CD81 large extracellular loop in complex with 5A6 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U9S
- Type
- protein
- Length
- 1,060 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5A6 Fab heavy chain; 5A6 Fab light chain; CD81 antigen
- UniProt
- P60033
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 16% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5A6 Fab heavy chain | protein | 221 | 7% helix, 52% strand | — |
| B | 5A6 Fab light chain | protein | 219 | 5% helix, 51% strand | — |
| C | CD81 antigen | protein | 92 | 64% helix, 0% strand | P60033 |
| D | 5A6 Fab heavy chain | protein | 218 | 7% helix, 52% strand | — |
| E | 5A6 Fab light chain | protein | 218 | 5% helix, 52% strand | — |
| F | CD81 antigen | protein | 92 | 62% helix, 0% strand | P60033 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.76 | 0.78 | 109 | GOL |
| 2 | 159 | 0.53 | 0.80 | 37 | empty |
| 3 | 192 | 0.51 | 0.77 | 33 | empty |
| 4 | 178 | 0.50 | 0.77 | 29 | empty |
| 5 | 155 | 0.49 | 0.78 | 31 | GOL |
Interfaces
10 interfaces between chains.
- A–B · 1893 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1724 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 627 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 627 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 535 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6U9S · Crystal structure of human CD81 large extracellular loop in complex with 5A6 Fab · the same entry in another collection · chain F against F, TM-score 1.00
- P60033 · AlphaFold monomer V2.0 prediction for CD81 antigen (P60033) · a predicted model of the same protein · chain C against A, TM-score 0.80
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 P60033
- Elsewhere: RCSB PDB 6U9S · PDBe 6U9S · UniProt P60033
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