Research workbench
Crystal structure of human CD81 large extracellular loop in complex with murine Fab fragment K04
Analyse Crystal structure of human CD81 large extracellular loop in complex with murine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DFV
- Type
- protein
- Length
- 1,036 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD81 antigen; Fab heavy chain; Fab light chain
- UniProt
- P60033
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CD81 antigen | protein | 88 | 64% helix, 0% strand | P60033 |
| B | CD81 antigen | protein | 86 | 73% helix, 0% strand | P60033 |
| C, E | Fab heavy chain | protein | 214 | 6% helix, 49% strand | — |
| D, F | Fab light chain | protein | 217 | 6% helix, 45% strand | — |
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.63 | 0.74 | 61 | empty |
| 2 | 497 | 0.59 | 0.74 | 56 | empty |
| 3 | 136 | 0.47 | 0.78 | 23 | empty |
| 4 | 145 | 0.43 | 0.75 | 24 | empty |
| 5 | 108 | 0.36 | 0.74 | 20 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1858 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1822 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 983 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 458 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 450 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- P60033 · AlphaFold monomer V2.0 prediction for CD81 antigen (P60033) · a predicted model of the same protein · chain B against A, TM-score 0.82
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 5DFV · PDBe 5DFV · UniProt P60033
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