6FLB: 3H5 Fab

3H5 Fab bound to EDIII of DenV 2 Xtal form 2. Determined by X-ray diffraction at 2.2 Å resolution. Released 24 Oct 2018.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Dengue virus 2, Mus musculus
Chains: 3
Atoms: 4,499
Mol. weight: 60.04 kDa
Ligands: PO4
Released: 24 Oct 2018

Explore 6FLB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6FLB contains 19 α-helices and 56 β-strands across 3 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 G: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	299-300	2
β-strand	301	1	1
α-helix	302	1
β-strand	305-314	10	2
β-strand	320-327	8	2
β-strand	333-334	2	1
α-helix	335-336	2
β-strand	337-340	4	3
β-strand	347-348	2	3
β-strand	350-351	2	2
β-strand	357-358	2	1
β-strand	365-370	6	2
α-helix	371-372	2
β-strand	374-380	7	3
β-strand	387-393	7	3

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	4
α-helix	7-9	3
β-strand	10-12	3	5
β-strand	18-25	8	4
α-helix	29-31	3
β-strand	33-39	7	5
β-strand	45-52	8	5
β-strand	57-60	4	5
α-helix	62-64	3
β-strand	68-73	6	4
β-strand	78-83	6	4
α-helix	88-90	3
β-strand	92-99	8	5
β-strand	106-107	2	5
β-strand	111-115	5	5
α-helix	118-120	3
β-strand	121	1	6
β-strand	124-128	5	7
β-strand	139-149	11	7
β-strand	150	1	6
β-strand	155-158	4	8
α-helix	159-161	3
β-strand	163	1	8
β-strand	167-169	3	7
α-helix	170-172	3
β-strand	173-175	3	7
β-strand	178-188	11	7
β-strand	198-203	6	8
α-helix	204-206	3
β-strand	208-213	6	8

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	10-14	5	10
β-strand	19-25	7	9
β-strand	30-31	2	11
β-strand	34-35	2	11
β-strand	37-42	6	10
β-strand	49-53	5	10
β-strand	57-58	2	10
α-helix	59	1
β-strand	66-71	6	9
β-strand	74-79	6	9
α-helix	84-86	3
β-strand	88-94	7	10
α-helix	100	1
β-strand	101-102	2	10
β-strand	106-111	6	10
β-strand	115	1	12
β-strand	118-122	5	13
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	13
β-strand	144	1	12
β-strand	149-154	6	14
β-strand	157-159	3	14
β-strand	163-167	5	13
α-helix	168-171	4
β-strand	177-186	10	13
α-helix	187-191	5
β-strand	195-201	7	14
β-strand	209-214	6	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Domain III of Dengue virus 2	G	protein	100	Dengue virus 2	P14340
Heavy chain of 3H5 Fab	H	protein	227	Mus musculus
Light chain of 3H5 Fab	L	protein	218	Mus musculus

Sequence of entity 1 (G), FASTA

>6FLB_1 Domain III of Dengue virus 2 (chains G)
SYSMCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPI
VTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKGSS

Sequence of entity 2 (H), FASTA

>6FLB_2 Heavy chain of 3H5 Fab (chains H)
QVQLQQSGAEVARPGASVKLSCKASGYTFTSYWLQWVKQRPGQGLEWIGAIWPGDDDTRY
AQKFQGKATMTADKSSSTAYIQLSNLASEDSAVYYCARKGGFAMDYWGQGTSVTVSSAKT
TPPSVYPLAPGSGAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYT
LSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIEPRDCGKHHHHHH

Sequence of entity 3 (L), FASTA

>6FLB_3 Light chain of 3H5 Fab (chains L)
NIVMTQSPTSLAVSLGQRATISCRASESVDSFGKSFMHFYQQKPGQPPKLLIHLASNLES
GVPARFTGRGSRTDFTLTIDPVEADDAATYYCQQNNEVPFTFGSGTKLEVKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

Water and common crystallization additives (CL, GOL) are not listed.

Primary citation

Characterization of a potent and highly unusual minimally enhancing antibody directed against dengue virus. Renner, M., Flanagan, A., Dejnirattisai, W. et al. Nat Immunol (2018) 19:1248-1256. DOI 10.1038/s41590-018-0227-7 · PubMed

Other PDB entries of the same protein (UniProt P14340), best resolution first:

6FLC 2.0 Å, 2C8 Fab bound to EDIII of DenV 2
6IZY 2.11 Å, The RNA-dependent RNA polymerase domain of dengue 2 NS5
6IZX 2.43 Å, The RNA-dependent RNA polymerase domain of dengue 2 NS5, bound with RK-0404678
6FLA 2.9 Å, 3H5 Fab bound to EDIII of DenV 2 Xtal form 1
7V3F 3.1 Å, DENV2_NGC_Fab_C10 28degree (1Fab:3E)
7V3G 3.3 Å, DENV2_NGC_Fab_C10 28degrees (2Fab:3E)
7CTH 3.5 Å, Cryo-EM structure of dengue virus serotype 2 in complex with the scFv fragment of the…
3J27 3.6 Å, CryoEM structure of Dengue virus
3J2P 3.6 Å, CryoEM structure of Dengue virus envelope protein heterotetramer
7V3H 3.6 Å, DENV2_NGC_Fab_C10 28degrees (3Fab:3E)
9DTT 3.6 Å, Cryo-EM structure of DENV2 NS5 in complex with Stem Loop A (SLA)
4CBF 4.1 Å, Near-atomic resolution cryo-EM structure of Dengue serotype 4 virus

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