MolNFT v1 · #12502 · protein
Fv mutant Y(A 50)S (vl domain) of mouse monoclonal antibody D1.3 complexed with hen egg white lysozyme
1KIR: “Fv mutant Y(A 50)S (vl domain) of mouse monoclonal antibody D1.3 complexed with hen egg white lysozyme”. X-ray diffraction, 3 pockets (best druggability 0.67). MolNFT v1 #12502 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1KIR
- 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
- 3 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 16% 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 | 38% helix, 10% 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 | 55 | 0.67 | 0.96 | 19 | empty |
| 2 | 64 | 0.44 | 0.82 | 22 | empty |
| 3 | 72 | 0.33 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 826 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 446 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 373 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1KIR · Fv mutant Y(A 50)S (vl domain) of mouse monoclonal antibody D1.3 complexed with hen egg… · the same entry in another collection · chain B against B, 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 1KIR · PDBe 1KIR · UniProt P00698
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