6H2Y: Human Fab 1E6

human Fab 1E6 bound to fHbp variant 3 from Neisseria meningitidis serogroup B. Determined by X-ray diffraction at 2.65 Å resolution. Released 14 Aug 2019.

Method: X-ray diffraction
Resolution: 2.65 Å
Organisms: Neisseria meningitidis, Homo sapiens
Chains: 3
Atoms: 5,135
Mol. weight: 78 kDa
Ligands: P33
Released: 14 Aug 2019

Explore 6H2Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6H2Y contains 19 α-helices and 65 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 D: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	38-39	2	1
α-helix	45	1
β-strand	49-54	6	2
β-strand	57-62	6	2
β-strand	69-70	2	1
α-helix	72-74	3
β-strand	80-89	10	2
β-strand	96-107	12	2
β-strand	111-122	12	2
β-strand	130-143	14	2
β-strand	145	1	3
α-helix	146	1
β-strand	147	1	4
β-strand	157-164	8	3
β-strand	167-175	9	3
β-strand	185-188	4	3
β-strand	198-206	9	3
β-strand	211	1	4
β-strand	212-219	8	3
β-strand	227-229	3	3
β-strand	232-233	2	3
β-strand	239-248	10	3
β-strand	251-261	11	3

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	5
β-strand	10-12	3	6
β-strand	18-24	7	5
β-strand	34-39	6	6
β-strand	45-52	8	6
β-strand	57-60	4	6
β-strand	68-73	6	5
β-strand	78-83	6	5
α-helix	88-90	3
β-strand	92-98	7	6
β-strand	108-109	2	6
β-strand	113-117	5	6
α-helix	121-122	2
β-strand	123	1	7
α-helix	124-125	2
β-strand	126-130	5	8
β-strand	142-151	10	8
β-strand	152	1	7
β-strand	157-160	4	9
α-helix	161-163	3
β-strand	165	1	9
β-strand	169-171	3	8
α-helix	172-174	3
β-strand	175-176	2	8
β-strand	182-190	9	8
α-helix	193-196	4
β-strand	201-206	6	9
α-helix	207-209	3
β-strand	211-216	6	9
α-helix	218-220	3

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	10
β-strand	9-12	4	11
β-strand	18-23	6	10
α-helix	27-29	3
β-strand	33-37	5	11
β-strand	44-47	4	11
β-strand	48	1	12
β-strand	52	1	12
β-strand	61-66	6	10
β-strand	69-74	6	10
α-helix	79-81	3
β-strand	83-91	9	11
β-strand	96-99	4	11
β-strand	103-107	5	11
α-helix	110-112	3
β-strand	113	1	13
α-helix	114-115	2
β-strand	116-120	5	14
α-helix	121-123	3
α-helix	124-128	5
β-strand	132-141	10	14
β-strand	142	1	13
β-strand	147-152	6	15
β-strand	155-157	3	15
β-strand	161-163	3	14
α-helix	164-166	3
β-strand	167-168	2	14
β-strand	174-182	9	14
α-helix	184-188	5
β-strand	193-199	7	15
β-strand	202-208	7	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lipoprotein GNA1870	D	protein	275	Neisseria meningitidis	Q19KF7 (AlphaFold model)
Heavy chain	H	protein	224	Homo sapiens
Light chain	L	protein	216	Homo sapiens

Sequence of entity 1 (D), FASTA

>6H2Y_1 Lipoprotein GNA1870 (chains D)
MGPDSDRLQQRRVAADIGTGLADALTAPLDHKDKGLKSLTLEDSIPQNGTLTLSAQGAEK
TFKAGDKDNSLNTGKLKNDKISRFDFVQKIEVDGQTITLASGEFQIYKQNHSAVVALQIE
KINNPDKTDSLINQRSFLVSGLGGEHTAFNQLPGGKAEYHGKAFSSDDPNGRLHYSIDFT
KKQGYGRIEHLKTLEQNVELAAAELKADEKSHAVILGDTRYGSEEKGTYHLALFGDRAQE
IAGSATVKIGEKVHEIGIAGKQKLAAALEHHHHHH

Sequence of entity 2 (H), FASTA

>6H2Y_2 Heavy chain (chains H)
EVQLVQSGAEVKKPGSSVKVSCKASGGTVIDYPITWVRQAPGQGLEWVGGFVPLFRTSNY
GQKFQGRVTITADKSTSTASMELNSLTSEDTAIYYCARGDTAMGPFDYWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Sequence of entity 3 (L), FASTA

>6H2Y_3 Light chain (chains L)
VVSYVLTQPPSLSVAPGKTATLTCGGNNIAGKTVHWYQQRPGQAPVLVISYDSDRPSGIP
ERFSGSNSANTATLTISRVEAGDEADYYCQVWDRNSDHWVFGGGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
P33	3,6,9,12,15,18-hexaoxaicosane-1,20-diol	C14 H30 O8	1

Water and common crystallization additives (EDO, PG4, PEG) are not listed.

Primary citation

Cocrystal structure of meningococcal factor H binding protein variant 3 reveals a new crossprotective epitope recognized by human mAb 1E6. Bianchi, F., Veggi, D., Santini, L. et al. FASEB J (2019) 33:12099-12111. DOI 10.1096/fj.201900374R · PubMed

Other PDB entries of the same protein (UniProt Q19KF7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4AYI 2.31 Å, Structure of a complex between CCPs 6 and 7 of Human Complement Factor H and Neisseria…
4AYM 3.0 Å, Structure of a complex between CCPs 6 and 7 of Human Complement Factor H and Neisseria…

Browse structure collections

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