Research workbench
Crystal structure of human CD81 large extracellular loop in complex with single chain fv fragment 4
Analyse Crystal structure of human CD81 large extracellular loop in complex with single… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EJG
- Type
- protein
- Length
- 640 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD81 antigen; Single chain fv fragment
- UniProt
- P60033
- Pockets
- 8 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | CD81 antigen | protein | 89 | 70% helix, 0% strand | P60033 |
| C, D | Single chain fv fragment | protein | 231 | 4% helix, 48% strand | — |
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.39 | 0.75 | 21 | empty |
| 2 | 91 | 0.37 | 0.76 | 20 | empty |
| 3 | 57 | 0.33 | 0.77 | 14 | empty |
| 4 | 92 | 0.32 | 0.73 | 20 | empty |
| 5 | 53 | 0.31 | 0.76 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 972 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 900 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 868 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 61 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6EJG · Crystal structure of human CD81 large extracellular loop in complex with single chain fv… · the same entry in another collection · chain A against A, TM-score 1.00
- P60033 · AlphaFold monomer V2.0 prediction for CD81 antigen (P60033) · a predicted model of the same protein · chain A against A, TM-score 0.83
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 6EJG · PDBe 6EJG · UniProt P60033
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