4U6V: Fab, antigen binding fragment, heavy chain

Mechanisms of Neutralization of a Human Anti-Alpha Toxin Antibody. Determined by X-ray diffraction at 2.56 Å resolution. Released 17 Sept 2014.

Method: X-ray diffraction
Resolution: 2.56 Å
Organisms: Homo sapiens, Staphylococcus aureus subsp. aureus TCH60
Chains: 6
Atoms: 11,052
Mol. weight: 161.58 kDa
Released: 17 Sept 2014

Explore 4U6V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4U6V contains 35 α-helices and 130 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.

Chains A and B: 3 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	18-29	12	12
β-strand	34-45	12	12
β-strand	50-62	13	12
β-strand	66-72	7	13
β-strand	75-89	15	13
β-strand	97-102	6	12
β-strand	107	1	13
β-strand	111-118	8	14
β-strand	124-125	2	14
β-strand	140-149	10	14
β-strand	153-158	6	13
β-strand	164-171	8	13
β-strand	174-176	3	15
β-strand	179-182	4	15
β-strand	192	1	13
β-strand	197	1	16
α-helix	206-208	3
β-strand	210	1	16
α-helix	211-212	2
α-helix	213-215	3
β-strand	223-224	2	12
β-strand	228-235	8	12
β-strand	242-260	19	13
β-strand	265-285	21	13
β-strand	290-292	3	13

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	57-58	2	3
β-strand	67-72	6	1
α-helix	73-75	3
β-strand	77-82	6	1
α-helix	87-89	3
β-strand	91-100	10	3
β-strand	106-112	7	3
β-strand	116-118	3	3
β-strand	119-120	2	2
α-helix	123-125	3
β-strand	126	1	4
α-helix	127-128	2
β-strand	129-133	5	5
β-strand	144-154	11	5
β-strand	155	1	4
β-strand	160-163	4	6
β-strand	172-174	3	5
α-helix	175-177	3
β-strand	178-179	2	5
β-strand	185-194	10	5
α-helix	195-198	4
β-strand	203-209	7	6
α-helix	210-212	3
β-strand	214-220	7	6

Chain K: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	11-12	2	18
β-strand	18-25	8	17
α-helix	29-31	3
β-strand	34-39	6	19
β-strand	45-51	7	19
β-strand	57-58	2	19
β-strand	67-72	6	17
α-helix	73-75	3
β-strand	77-82	6	17
α-helix	87-89	3
β-strand	91-100	10	19
β-strand	106-112	7	19
β-strand	116-118	3	19
β-strand	119-120	2	18
α-helix	123-125	3
β-strand	126	1	20
α-helix	127-128	2
β-strand	129-133	5	21
β-strand	144-154	11	21
β-strand	155	1	20
β-strand	160-163	4	22
α-helix	164-166	3
β-strand	172-174	3	21
α-helix	175-177	3
β-strand	178-179	2	21
β-strand	185-194	10	21
α-helix	195-197	3
β-strand	203-209	7	22
α-helix	210-212	3
β-strand	214-220	7	22

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	85-90	6	8
β-strand	96-97	2	8
β-strand	101-105	5	8
β-strand	110	1	9
α-helix	111-112	2
β-strand	113-117	5	10
α-helix	121-126	6
β-strand	128-138	11	10
β-strand	139	1	9
β-strand	144-149	6	11
β-strand	152-153	2	11
β-strand	158-162	5	10
α-helix	163-166	4
β-strand	172-181	10	10
α-helix	182-185	4
β-strand	190-196	7	11
β-strand	204-209	6	11

Chain M: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	23
β-strand	10-13	4	24
β-strand	19-25	7	23
β-strand	33-38	6	24
β-strand	45-49	5	24
β-strand	53-54	2	24
α-helix	55	1
β-strand	62-67	6	23
β-strand	70-75	6	23
α-helix	80-82	3
β-strand	85-90	6	24
β-strand	96-97	2	24
β-strand	101-105	5	24
β-strand	110	1	25
α-helix	111-112	2
β-strand	113-117	5	26
α-helix	121-125	5
β-strand	128-138	11	26
β-strand	139	1	25
β-strand	144-149	6	27
β-strand	152-153	2	27
β-strand	158-162	5	26
α-helix	163-166	4
β-strand	172-181	10	26
α-helix	182-185	4
β-strand	190-196	7	27
β-strand	204-209	6	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab, antigen binding fragment, heavy chain	H, K	protein	225	Homo sapiens
Fab, antigen binding fragment, light chain	L, M	protein	213	Homo sapiens
Alpha-hemolysin	A, B	protein	293	Staphylococcus aureus subsp. aureus TCH60	Q2G1X0 (AlphaFold model)

Sequence of entity 1 (H, K), FASTA

>4U6V_1 Fab, antigen binding fragment, heavy chain (chains H, K)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSSHDMHWVRQATGKGLEWVSGIGTAGDTYYP
DSVKGRFTISRENAKNSLYLQMNSLRAGDTAVYYCARDRYSPTGHYYGMDVWGQGTTVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 2 (L, M), FASTA

>4U6V_2 Fab, antigen binding fragment, light chain (chains L, M)
DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASSLESGVPS
RFSGSGSGTEFTLTISSLQPDDFATYYCKQYADYWTFGQGTKVEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (A, B), FASTA

>4U6V_3 Alpha-hemolysin (chains A, B)
ADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKGT
IAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYGF
NGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNWG
PYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRKASK
QQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWIDRSSERYKIDWEKEEMTN

Primary citation

Mechanisms of Neutralization of a Human Anti-alpha-toxin Antibody. Oganesyan, V., Peng, L., Damschroder, M.M. et al. J Biol Chem (2014) 289:29874-29880. DOI 10.1074/jbc.M114.601328 · PubMed

Other PDB entries of the same protein (UniProt Q2G1X0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9SHR 2.08 Å, Alpha-Hemolysin of S.aureus (monomer) in complex with the small molecule…
9KG0 2.6 Å, Alpha-hemolysin heptameric late pre-pore state derived from 10:0 PC/Sphingomyelin…
9KTO 2.6 Å, Alpha-hemolysin heptameric late pre-pore state with bound lipids derived from 10:0…
9KG6 2.8 Å, Alpha-hemolysin heptameric pore state derived from 10:0 PC liposomes
9KRF 2.8 Å, Alpha-hemolysin heptameric pore state bound to 10:0 PC lipid chains derived from 10:0 PC…
9KG1 2.9 Å, Alpha-hemolysin heptameric pre-pore state derived from 10:0 PC liposomes.
9KTM 2.9 Å, Alpha-hemolysin heptameric pre-pore state bound to 10:PC lipid chains derived from 10:0…
9KRE 3.0 Å, Alpha-hemolysin heptameric POPC bound pore state derived from egg PC/Cholesterol (3:1…
9KG3 3.07 Å, Alpha-hemolysin heptameric pore state derived from egg PC/Cholesterol (3:1 molar ratio)…
7O1Q 3.4 Å, Amyloid beta oligomer displayed on the alpha hemolysin scaffold

Browse structure collections

About this viewer

MolViewer shows 4U6V 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.