Research workbench
B1-8 fv fragment complexed with a (4-hydroxy-3-nitrophenyl) acetate compound
Analyse B1-8 fv fragment complexed with a (4-hydroxy-3-nitrophenyl) acetate compound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1A6V
- Type
- protein
- Length
- 685 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B1-8 fv (light chain); B1-8 fv (heavy chain)
- UniProt
- P01724, P01751
- Ligands
- NPC
- Pockets
- 8 · best druggability 0.56
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | B1-8 fv (light chain) | protein | 110 | 5% helix, 54% strand | P01724 |
| H | B1-8 fv (heavy chain) | protein | 118 | 5% helix, 47% strand | P01751 |
| M, N | B1-8 fv (light chain) | protein | 109 | 3% helix, 50% strand | P01724 |
| I | B1-8 fv (heavy chain) | protein | 119 | 5% helix, 51% strand | P01751 |
| J | B1-8 fv (heavy chain) | protein | 120 | 3% helix, 41% strand | P01751 |
Ligands and binding sites
- NPC · 4-hydroxy-3-nitrophenylacetyl-epsilon-aminocaproic acid anion · ligand · 3 copies · chains L, H, M, I, N, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.56 | 0.74 | 43 | empty |
| 2 | 361 | 0.56 | 0.75 | 45 | empty |
| 3 | 116 | 0.44 | 0.77 | 17 | NPC |
| 4 | 91 | 0.41 | 0.78 | 17 | empty |
| 5 | 54 | 0.34 | 0.77 | 12 | NPC |
Interfaces
5 interfaces between chains.
- L–H · 941 Ų buried · 10 hydrogen bonds · protein-protein
- M–I · 940 Ų buried · 9 hydrogen bonds · protein-protein
- N–J · 901 Ų buried · 16 hydrogen bonds · protein-protein
- I–J · 317 Ų buried · 1 hydrogen bond · protein-protein
- H–I · 261 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1A6V · B1-8 FV fragment complexed with a (4-hydroxy-3-nitrophenyl) acetate compound · the same entry in another collection · chain J against J, TM-score 1.00
- P01724 · AlphaFold monomer V2.0 prediction for ig lambda-1 chain V regions mopc… · a predicted model of the same protein · chain M against A, TM-score 0.98
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 P01724
- Every structure of UniProt P01751
- Elsewhere: RCSB PDB 1A6V · PDBe 1A6V · UniProt P01724 · UniProt P01751
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