MolNFT v1 · #25090 · protein
Bound water molecules and conformational stabilization help mediate an antigen-antibody association
1VFB · IGG1-kappa D1.3 fv (light chain): “Bound water molecules and conformational stabilization help mediate an antigen-antibody association”. X-ray diffraction, 3 pockets (best druggability 0.71). MolNFT v1 #25090 on GenesisL1: 3D…
- PDB
- 1VFB
- Type
- protein
- Length
- 352 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1-kappa D1.3 fv (light chain); IGG1-kappa D1.3 fv (heavy chain); Hen egg white lysozyme
- UniProt
- P00698
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IGG1-kappa D1.3 fv (light chain) | protein | 107 | 3% helix, 50% strand | — |
| B | IGG1-kappa D1.3 fv (heavy chain) | protein | 116 | 5% helix, 52% strand | — |
| C | Hen egg white lysozyme | protein | 129 | 40% helix, 11% strand | P00698 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.71 | 0.94 | 22 | empty |
| 2 | 90 | 0.34 | 0.74 | 20 | empty |
| 3 | 52 | 0.23 | 0.72 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 841 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 435 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 385 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1VFB · Bound water molecules and conformational stabilization help mediate an antigen-antibody… · the same entry in another collection · chain A against A, 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
- Every structure of UniProt P00698
- Elsewhere: RCSB PDB 1VFB · PDBe 1VFB · UniProt P00698
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