MolNFT v1 · #46070 · protein
Crystal structure of a quorum-quenching antibody in complex with an N- acyl-L-homoserine lactone analog
2NTF · Murine antibody Fab RS2-1G9 lambda light chain: “Crystal structure of a quorum-quenching antibody in complex with an N- acyl-L-homoserine lactone analog”. X-ray diffraction, 1 ligand (OHM), 12 pockets (best druggability 0.74).…
- PDB
- 2NTF
- Type
- protein
- Length
- 866 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Murine antibody Fab RS2-1G9 lambda light chain; Murine antibody Fab RS2-1G9 IGG1 heavy…
- UniProt
- Q0VDX6, Q99LC4
- Ligands
- OHM
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Murine antibody Fab RS2-1G9 lambda light chain | protein | 211 | 8% helix, 54% strand | Q0VDX6 |
| H, B | Murine antibody Fab RS2-1G9 IGG1 heavy chain | protein | 222 | 7% helix, 51% strand | Q99LC4 |
Ligands and binding sites
- OHM · 3-oxo-N-[(3S)-2-oxopyrrolidin-3-yl]dodecanamide · ligand · 2 copies · chains L, H, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.74 | 0.82 | 71 | OHM |
| 2 | 299 | 0.74 | 0.86 | 54 | OHM |
| 3 | 338 | 0.60 | 0.77 | 36 | empty |
| 4 | 152 | 0.58 | 0.83 | 24 | empty |
| 5 | 161 | 0.58 | 0.82 | 26 | empty |
Interfaces
6 interfaces between chains.
- L–H · 2024 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2005 Ų buried · 11 hydrogen bonds · protein-protein
- L–A · 820 Ų buried · 8 hydrogen bonds · protein-protein
- H–A · 191 Ų buried · 3 hydrogen bonds · protein-protein
- H–B · 166 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2NTF · Crystal Structure of a Quorum-Quenching Antibody in Complex with an N-Acyl-L-Homoserine… · the same entry in another collection · chain L against L, 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 Q0VDX6
- Every structure of UniProt Q99LC4
- Elsewhere: RCSB PDB 2NTF · PDBe 2NTF · UniProt Q0VDX6 · UniProt Q99LC4
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