MolNFT v1 · #30535 · protein
Anti-cocaine antibody 7.5.21, crystal form I
2A1W · Immunoglobulin light chain kappa: “Anti-cocaine antibody 7.5.21, crystal form I”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.75). MolNFT v1 #30535 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2A1W
- Type
- protein
- Length
- 882 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin light chain kappa; Immunoglobulin heavy chain
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Immunoglobulin light chain kappa | protein | 216 | 6% helix, 50% strand | — |
| H, I | Immunoglobulin heavy chain | protein | 225 | 5% helix, 49% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains L, M, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.75 | 0.83 | 72 | SO4 |
| 2 | 525 | 0.62 | 0.75 | 62 | empty |
| 3 | 408 | 0.60 | 0.76 | 53 | empty |
| 4 | 189 | 0.52 | 0.78 | 31 | empty |
| 5 | 107 | 0.45 | 0.79 | 20 | empty |
Interfaces
6 interfaces between chains.
- M–I · 2090 Ų buried · 15 hydrogen bonds · protein-protein
- L–H · 1869 Ų buried · 18 hydrogen bonds · protein-protein
- L–I · 299 Ų buried · 1 hydrogen bond · protein-protein
- H–M · 186 Ų buried · 0 hydrogen bonds · protein-protein
- H–I · 87 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2A1W · Anti-cocaine antibody 7.5.21, crystal form I · the same entry in another collection · chain L against L, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 2A1W · PDBe 2A1W
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