MolNFT v1 · #12500 · protein
Fv mutant Y(B 32)A (vh domain) of mouse monoclonal antibody D1.3 complexed with hen egg white lysozyme
1KIP: “Fv mutant Y(B 32)A (vh domain) of mouse monoclonal antibody D1.3 complexed with hen egg white lysozyme”. X-ray diffraction, 4 pockets (best druggability 0.64). MolNFT v1 #12500 on GenesisL1: 3D structure, binding sites and pockets…
- 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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