MolNFT v1 · #12658 · protein
Crystal structure of the complex of a catalytic antibody Fab with a transition state analog: structural similarities in esterase-like abzymes
1KNO · IGG2A Fab fragment CNJ206: “Crystal structure of the complex of a catalytic antibody Fab with a transition state analog: structural…”. X-ray diffraction, 2 ligands (PNP, ZN), 17 pockets (best druggability 0.74). MolNFT v1 #12658 on…
- PDB
- 1KNO
- Type
- protein
- Length
- 1,302 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2A Fab fragment CNJ206
- Ligands
- PNP, ZN
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | IGG2A Fab fragment CNJ206 | protein | 214 | 6% helix, 49% strand | — |
| B, D, F | IGG2A Fab fragment CNJ206 | protein | 220 | 8% helix, 48% strand | — |
Ligands and binding sites
- PNP · Methyl-phosphonic acid mono-(4-nitro-phenyl) ester · ligand · 3 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 928 | 0.74 | 0.78 | 86 | empty |
| 2 | 901 | 0.73 | 0.77 | 85 | empty |
| 3 | 71 | 0.62 | 0.90 | 16 | PNP |
| 4 | 74 | 0.62 | 0.90 | 16 | PNP |
| 5 | 80 | 0.62 | 0.89 | 20 | PNP |
Interfaces
7 interfaces between chains.
- C–D · 1936 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1932 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1919 Ų buried · 21 hydrogen bonds · protein-protein
- B–F · 441 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 285 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1KNO · Crystal structure of the complex of a catalytic antibody Fab with a transition state… · 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
- Elsewhere: RCSB PDB 1KNO · PDBe 1KNO
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