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Fv mutant Y(B 32)A (vh domain) of mouse monoclonal antibody D1.3 complexed with hen egg white lysozyme
Analyse Fv mutant Y(B 32)A (vh domain) of mouse monoclonal antibody D1.3 complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KIP
- Type
- protein
- Length
- 352 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoclonal antibody D1.3; Lysozyme
- EC
- 3.2.1.17
- UniProt
- P00698
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Monoclonal antibody D1.3 | protein | 107 | 3% helix, 50% strand | — |
| B | Monoclonal antibody D1.3 | protein | 116 | 5% helix, 52% strand | — |
| C | Lysozyme (EC 3.2.1.17) | protein | 129 | 39% helix, 11% strand | P00698 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.64 | 0.89 | 26 | empty |
| 2 | 58 | 0.39 | 0.80 | 14 | empty |
| 3 | 56 | 0.27 | 0.74 | 15 | empty |
| 4 | 53 | 0.24 | 0.72 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 822 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 398 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 350 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1KIP · Fv mutant Y(B 32)A (vh domain) of mouse monoclonal antibody D1.3 complexed with hen egg… · 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 1KIP · PDBe 1KIP · UniProt P00698
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