MolNFT v1 · #126497 · protein
Structural tuning of CD81LEL (space group C2)
5M4R · CD81 antigen: “Structural tuning of CD81LEL (space group C2)”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.37). MolNFT v1 #126497 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5M4R
- Type
- protein
- Length
- 432 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD81 antigen
- UniProt
- P60033
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.37
Structure
x-ray diffraction · 5 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CD81 antigen | protein | 86 | 70% helix, 0% strand | P60033 |
| B | CD81 antigen | protein | 87 | 66% helix, 0% strand | P60033 |
| C | CD81 antigen | protein | 86 | 71% helix, 0% strand | P60033 |
| D | CD81 antigen | protein | 86 | 63% helix, 0% strand | P60033 |
| E | CD81 antigen | protein | 87 | 67% helix, 0% strand | P60033 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains B, C, E
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.37 | 0.74 | 19 | empty |
| 2 | 65 | 0.35 | 0.76 | 14 | EDO |
| 3 | 74 | 0.33 | 0.75 | 15 | empty |
Interfaces
5 interfaces between chains.
- B–E · 837 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 778 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 330 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 236 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 187 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
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 5M4R · PDBe 5M4R · UniProt P60033
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