2NTF: Quorum-Quenching Antibody

Crystal Structure of a Quorum-Quenching Antibody in Complex with an N-Acyl-L-Homoserine Lactone Analog. Determined by X-ray diffraction at 3.18 Å resolution. Released 8 May 2007.

Method: X-ray diffraction
Resolution: 3.18 Å
Organism: Mus musculus
Chains: 4
Atoms: 6,652
Mol. weight: 94.44 kDa
Ligands: OHM
Released: 8 May 2007

Explore 2NTF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2NTF contains 25 α-helices and 91 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	11
β-strand	9-13	4	12
β-strand	19-23	5	13
β-strand	24-25	2	11
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	43-49	7	12
β-strand	53-54	2	12
α-helix	55	1
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	84-91	8	12
β-strand	96-98	3	12
β-strand	102-106	5	12
β-strand	111	1	14
β-strand	117-118	2	15
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	15
β-strand	140	1	14
β-strand	145-150	6	16
β-strand	153-154	2	16
β-strand	159-161	3	15
α-helix	162-164	3
β-strand	165-166	2	15
β-strand	173-182	10	15
α-helix	183-188	6
β-strand	191-198	8	16
β-strand	203-210	8	16

Chains B and H: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	17
β-strand	9-12	4	18
β-strand	18-25	8	17
α-helix	29-31	3
β-strand	32-39	8	18
β-strand	46-52	7	18
β-strand	56-59	4	18
α-helix	61-63	3
β-strand	67-70	4	17
β-strand	77-82	6	17
α-helix	84-86	3
β-strand	88-97	10	18
β-strand	102-103	2	18
β-strand	107-111	5	18
β-strand	117	1	19
β-strand	120-124	5	20
β-strand	137-147	11	20
β-strand	148	1	19
β-strand	153-157	4	21
α-helix	162-164	3
β-strand	166	1	21
β-strand	171-173	3	20
β-strand	177-181	3	20
β-strand	184-194	11	20
β-strand	206-212	6	21
α-helix	213-215	3
β-strand	217-222	6	21

Chain L: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	9-13	4	2
β-strand	19-25	7	1
β-strand	27A	1	1
α-helix	27C-28	2
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	43-49	7	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-91	8	2
β-strand	96-98	3	2
β-strand	102-106	5	2
β-strand	111	1	3
β-strand	114	1	4
β-strand	117-118	2	4
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-154	2	5
β-strand	159-161	3	4
α-helix	162-164	3
β-strand	165-166	2	4
β-strand	173-182	10	4
α-helix	183-188	6
β-strand	191-198	8	5
β-strand	203-210	8	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Murine Antibody Fab RS2-1G9 Lambda Light Chain	A, L	protein	211	Mus musculus	G0YP42 (AlphaFold model)
Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain	B, H	protein	222	Mus musculus	P01868 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>2NTF_1 Murine Antibody Fab RS2-1G9 Lambda Light Chain (chains A, L)
QAVVTQESALTTSPGETVTLTCRSSTGAVTTRNYANWVQEKPDHFFTGLIGDTNNRAPGV
PARFSGSLIGHKAALTITGAQTEDESVYFCALWYSNHWVFGGGTKLTVLGQPKSSPSVTL
FPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSY
LTLTAGAWERHSSYSCQVTHEGHTVEKSLSR

Sequence of entity 2 (B, H), FASTA

>2NTF_2 Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain (chains B, H)
QVQLQQSGSELVRPGASVKLSCKASGYTFTTYWIHWVKQRPGQGLEWIGTIYPGSDNTYY
DEKFKNKATLTVDTSSSTAFMQLSSLTSEDSAVYFCTRGSLYYNNYGWFGYWGQGTLVTV
SAAKTTPPSVYPLAPGSNAASQSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQ
SDLYTLTSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPR

Ligands and cofactors

ID	Name	Formula	Copies
OHM	3-oxo-N-[(3S)-2-oxopyrrolidin-3-yl]dodecanamide	C16 H28 N2 O3	2

Primary citation

Crystal Structures of a Quorum-quenching Antibody. Debler, E.W., Kaufmann, G.F., Kirchdoerfer, R.N. et al. J Mol Biol (2007) 368:1392-1402. DOI 10.1016/j.jmb.2007.02.081 · PubMed

Other PDB entries of the same protein (UniProt G0YP42 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1NGP 2.4 Å, N1G9 (IgG1-lambda) FAB fragment complexed with (4-hydroxy-3-nitrophenyl) acetate
1NGQ 2.4 Å, N1G9 (IgG1-lambda) FAB fragment
1PG7 2.5 Å, Murine 6A6 Fab in complex with humanized anti-Tissue Factor D3H44 Fab
1ETZ 2.6 Å, The three-dimensional structure of an anti-sweetener FAB, NC10.14, shows the extent of…
2OP4 2.85 Å, Crystal Structure of Quorum-Quenching Antibody 1G9
2VIR 3.25 Å, Influenza virus hemagglutinin complexed with a neutralizing antibody
2VIS 3.25 Å, Influenza virus hemagglutinin, (ESCAPE) mutant with thr 131 replaced by ile, complexed…
2VIT 3.25 Å, Influenza virus hemagglutinin, mutant with thr 155 replaced by ile, complexed with a…
3RHW 3.26 Å, C. elegans glutamate-gated chloride channel (GluCl) in complex with Fab and ivermectin
3RIF 3.35 Å, C. elegans glutamate-gated chloride channel (GluCl) in complex with Fab, ivermectin and…
3RI5 3.4 Å, C. elegans glutamate-gated chloride channel (GluCl) in complex with Fab, ivermectin and…
3RIA 3.8 Å, C. elegans glutamate-gated chloride channel (GluCl) in complex with Fab, ivermectin and…

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