MolNFT v1 · #116507 · protein
Crystal structure of human CD81 large extracellular loop in complex with murine Fab fragment K04
5DFV · CD81 antigen: “Crystal structure of human CD81 large extracellular loop in complex with murine Fab fragment K04”. X-ray diffraction, 10 pockets (best druggability 0.63). MolNFT v1 #116507 on GenesisL1: 3D structure, binding sites…
- 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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