MolNFT v1 · #84989 · protein
Crystallographic structure of the esterolytic and amidolytic 43C9 antibody with bound P-nitrophenol
43CA · Protein (immunoglobulin (light chain)): “Crystallographic structure of the esterolytic and amidolytic 43C9 antibody with bound P-nitrophenol”. X-ray diffraction, 1 ligand (NPO), 10 pockets (best druggability 0.58). MolNFT v1 #84989…
- PDB
- 43CA
- Type
- protein
- Length
- 920 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (immunoglobulin (light chain)); Protein (immunoglobulin (heavy chain))
- UniProt
- Q9ERZ9, P01820
- Ligands
- NPO
- Pockets
- 10 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Protein (immunoglobulin (light chain)) | protein | 113 | 3% helix, 50% strand | Q9ERZ9 |
| B, D, F, H | Protein (immunoglobulin (heavy chain)) | protein | 117 | 3% helix, 55% strand | P01820 |
Ligands and binding sites
- NPO · P-nitrophenol · ligand · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.58 | 0.83 | 22 | NPO |
| 2 | 126 | 0.57 | 0.83 | 19 | NPO |
| 3 | 134 | 0.56 | 0.82 | 21 | NPO |
| 4 | 110 | 0.55 | 0.83 | 19 | NPO |
| 5 | 143 | 0.53 | 0.80 | 28 | empty |
Interfaces
7 interfaces between chains.
- E–F · 839 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 833 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 831 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 817 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 586 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 43CA · Crystallographic structure of the esterolytic and amidolytic 43C9 antibody with bound… · the same entry in another collection · chain H against H, TM-score 1.00
- P01820 · AlphaFold monomer V2.0 prediction for ig heavy chain V region PJ14 (P01820) · a predicted model of the same protein · chain B against A, TM-score 0.78
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 Q9ERZ9
- Every structure of UniProt P01820
- Elsewhere: RCSB PDB 43CA · PDBe 43CA · UniProt Q9ERZ9 · UniProt P01820
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