5O1R: Human Fab 5H2

human Fab 5H2 bound to NHBA-C3 from Neisseria meningitidis serogroup B. Determined by X-ray diffraction at 2.86 Å resolution. Released 30 May 2018.

Method: X-ray diffraction
Resolution: 2.86 Å
Organisms: Neisseria meningitidis, Homo sapiens
Chains: 6
Atoms: 8,326
Mol. weight: 129.84 kDa
Released: 30 May 2018

Explore 5O1R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5O1R contains 32 α-helices and 106 β-strands across 6 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: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	316-326	11	1
α-helix	334	1
β-strand	336-345	10	1
β-strand	350-356	7	1
β-strand	365-373	9	1
β-strand	376-381	6	1
β-strand	386	1	2
β-strand	389-394	6	1
β-strand	400-407	8	1
β-strand	408	1	2
β-strand	416-424	9	1

Chain B: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	316-327	12	3
α-helix	334	1
β-strand	336-345	10	3
β-strand	350-356	7	3
β-strand	365-373	9	3
β-strand	376-381	6	3
β-strand	389-394	6	3
β-strand	400-406	7	3
β-strand	416-424	9	3

Chain H: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	11-12	2	5
β-strand	18-25	8	4
β-strand	34-42	9	6
β-strand	46-53	8	6
β-strand	59-61	3	6
β-strand	69-74	6	4
β-strand	79-84	6	4
α-helix	89-91	3
β-strand	93-103	11	6
β-strand	107-113	7	6
β-strand	117-119	3	6
β-strand	120-121	2	5
α-helix	125-126	2
β-strand	127	1	7
β-strand	130-134	5	8
α-helix	135-137	3
β-strand	145-155	11	8
β-strand	156	1	7
β-strand	161-164	4	9
α-helix	165-167	3
β-strand	169	1	9
β-strand	173-175	3	8
α-helix	176-178	3
β-strand	179-180	2	8
β-strand	186-195	10	8
α-helix	196-200	5
β-strand	205-210	6	9
α-helix	211-213	3
β-strand	215-220	6	9

Chain I: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	18-25	8	10
β-strand	34-42	9	12
β-strand	46-53	8	12
β-strand	59-61	3	12
β-strand	69-74	6	10
α-helix	75-77	3
β-strand	79-84	6	10
α-helix	89-91	3
β-strand	93-103	11	12
β-strand	107-113	7	12
β-strand	117-119	3	12
β-strand	120-121	2	11
α-helix	125-126	2
β-strand	127	1	13
β-strand	130-134	5	14
α-helix	135-137	3
β-strand	145-155	11	14
β-strand	156	1	13
β-strand	161-164	4	15
α-helix	165-167	3
β-strand	169	1	15
β-strand	173-175	3	14
α-helix	176-178	3
β-strand	179-180	2	14
β-strand	186-195	10	14
α-helix	196-200	5
α-helix	203	1
β-strand	204-210	7	15
α-helix	211-213	3
β-strand	215-221	7	15

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-14	5	17
β-strand	19-25	7	16
β-strand	33-38	6	17
β-strand	45-49	5	17
β-strand	53-54	2	17
α-helix	55	1
β-strand	62-67	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	84-90	7	17
β-strand	96-97	2	17
β-strand	101-106	6	17
β-strand	110	1	18
β-strand	113-117	5	19
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-138	11	19
β-strand	139	1	18
β-strand	143-149	7	20
β-strand	152-153	2	20
β-strand	158-162	5	19
α-helix	163-166	4
β-strand	172-181	10	19
α-helix	182-186	5
β-strand	191-197	7	20
β-strand	204-208	5	20

Chain M: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	21
β-strand	10-14	5	22
β-strand	19-25	7	21
β-strand	33-38	6	22
β-strand	45-49	5	22
β-strand	53-54	2	22
α-helix	55	1
β-strand	62-67	6	21
β-strand	70-75	6	21
α-helix	80-82	3
β-strand	84-90	7	22
β-strand	96-97	2	22
β-strand	101-106	6	22
β-strand	110	1	23
β-strand	113-117	5	24
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-138	11	24
β-strand	139	1	23
β-strand	143-149	7	25
β-strand	152-153	2	25
α-helix	154	1
β-strand	158-162	5	24
α-helix	163-166	4
β-strand	172-181	10	24
α-helix	182-186	5
β-strand	190-197	8	25
β-strand	204-209	6	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GNA2132	A, B	protein	127	Neisseria meningitidis	Q9JPP1 (AlphaFold model)
IGH@ protein	H, I	protein	265	Homo sapiens	Q6GMX6 (AlphaFold model)
Uncharacterized protein	L, M	protein	213	Homo sapiens	Q6GMX0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5O1R_1 GNA2132 (chains A, B)
MASMLAGTAVYNGEVLHFHTENGRPYPTRGRFAAKVDFGSKSVDGIIDSGDDLHMGTQKF
KAAIDGNGFKGTWTENGGGDVSGRFYGPAGEEVAGKYSYRPTDAEKGGFGVFAGKKEQDL
EHHHHHH

Sequence of entity 2 (H, I), FASTA

>5O1R_2 IGH@ protein (chains H, I)
QVQLQESGPGLVKPSETLSLTCTVSGGSVSSGSSYWTWIRQTPGKGLEWIGYTSYSGSTK
YNPSLKSRVTLSVDMSKNQFSLKLKSVTAADTAVYFCARDRFDVASGSSFDFWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKGSENLYFQGSWS
HPQFEKGGSGGGSGGGSWSHPQFEK

Sequence of entity 3 (L, M), FASTA

>5O1R_3 Uncharacterized protein (chains L, M)
EIVMTQTPSSLSASVGDRVTITCRASQSISNYLNWYQQKPGTAPKLLTYAASSLGSGVPS
RFSGSGSGTDLTLTISSLRPEDFATYYCQQSYGSPTFGQGTKLEIRRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Structures of NHBA elucidate a broadly conserved epitope identified by a vaccine induced antibody. Maritan, M., Veggi, D., Cozzi, R. et al. PLoS One (2018) 13:e0201922-e0201922. DOI 10.1371/journal.pone.0201922 · PubMed

Other PDB entries of the same protein (UniProt Q9JPP1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CUJ 1.8 Å, Crystal structure of the C-terminal domain of neisserial heparin binding antigen (NHBA)
2LFU The structure of a N. meningitides protein targeted for vaccine development

Browse structure collections

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