5TR8: 441D6 Fab Light chain

Crystal structure of vaccine-elicited pan- influenza H1N1 neutralizing murine antibody 441D6. Determined by X-ray diffraction at 2.01 Å resolution. Released 9 May 2018.

Method: X-ray diffraction
Resolution: 2.01 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,585
Mol. weight: 47.69 kDa
Ligands: NI
Released: 9 May 2018

Explore 5TR8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5TR8 contains 15 α-helices and 43 β-strands across 2 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 H: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	45-51	7	8
β-strand	57-59	3	8
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-95	8	8
β-strand	100B-103	4	8
β-strand	107-109	3	8
β-strand	110-111	2	7
α-helix	115-116	2
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
α-helix	125-127	3
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	159	1	11
β-strand	163-171	9	10
β-strand	174-184	11	10
β-strand	194-199	6	11
α-helix	200-202	3
β-strand	204-209	6	11

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	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	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-155	3	5
β-strand	159-163	5	4
β-strand	173-182	10	4
α-helix	183-186	4
β-strand	191-197	7	5
α-helix	204	1
β-strand	205-210	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
441D6 Fab Light chain	L	protein	212	Mus musculus	Q7TS98 (AlphaFold model)
441D6 Fab Heavy chain	H	protein	221	Mus musculus	A0A0E4B366 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>5TR8_1 441D6 Fab Light chain (chains L)
DIKMTQSPSSMYASLGERVTFTCKASQDIYSSFSWFQQRPGKSPKTLIYRANRLVDGVPS
RFSGSGSGQDYSLTISSLEYEDMGVYFCLQHEEFPPTFGGGTKLELKRTDAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

Sequence of entity 2 (H), FASTA

>5TR8_2 441D6 Fab Heavy chain (chains H)
EVQLVESGGGLMRPGGSLKLSCAASGFAFSRFDMSWVRQTPEKRLEWVAYIRNGADDTYY
ADTEKGRFTISRDNAKNTLYLQLSSLKIEDTAMYYCVRHSGYSYVIDYWGQGTSVTVSSA
STTAPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSGL
YTLSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIEPRVP

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	2

Primary citation

Mosaic nanoparticle display of diverse influenza virus hemagglutinins elicits broad B cell responses. Kanekiyo, M., Joyce, M.G., Gillespie, R.A. et al. Nat Immunol (2019) 20:362-372. DOI 10.1038/s41590-018-0305-x · PubMed

Other PDB entries of the same protein (UniProt Q7TS98 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VPL 1.9 Å, Crystal structure of der F 1 complexed with FAB 4C1
1JGL 2.15 Å, Crystal structure of immunoglobulin Fab fragment complexed with 17-beta-estradiol
1JHK 2.51 Å, Crystal structure of the anti-estradiol antibody 57-2

Browse structure collections

About this viewer

MolViewer shows 5TR8 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.