5WHK: Fab fragment of antibody DX-2507

Crystal structure of Fab fragment of antibody DX-2507 bound to FcRn-B2M. Determined by X-ray diffraction at 2.5 Å resolution. Released 6 Sept 2017.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,121
Mol. weight: 92.74 kDa
Ligands: NHE
Released: 6 Sept 2017

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

Secondary structure: helices and β-sheets

5WHK contains 25 α-helices and 77 β-strands across 4 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: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	10	14
α-helix	17-18	2
β-strand	24-30	7	14
β-strand	33-39	7	14
β-strand	46-47	2	14
α-helix	58-82	25
β-strand	89-98	10	14
β-strand	104-112	9	14
β-strand	115-121	7	14
β-strand	126-128	3	14
α-helix	132-142	11
α-helix	147-153	7
α-helix	154-158	5
α-helix	159-165	7
β-strand	178	1	15
α-helix	179-180	2
β-strand	181-190	10	16
β-strand	193-203	11	16
β-strand	204	1	15
β-strand	209-214	6	17
β-strand	217-219	3	17
β-strand	225-228	4	16
β-strand	234-243	10	16
α-helix	247-249	3
β-strand	250-255	6	17
β-strand	263-265	3	17
α-helix	266-268	3

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	18
α-helix	4-5	2
β-strand	6-11	6	19
β-strand	21-30	10	19
β-strand	31	1	18
β-strand	36-41	6	20
β-strand	44-45	2	20
β-strand	50-51	2	19
β-strand	55-56	2	19
β-strand	62-70	9	19
β-strand	78-83	6	20
β-strand	91-94	4	20

Chain H: 8 helices, 23 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	58-60	3	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	3
β-strand	106	1	3
β-strand	110-112	3	3
β-strand	113-114	2	2
α-helix	118-119	2
β-strand	120	1	4
α-helix	121-122	2
β-strand	123-127	5	5
β-strand	138-148	11	5
β-strand	149	1	4
β-strand	154-157	4	6
α-helix	158-160	3
β-strand	162	1	6
β-strand	166-168	3	5
α-helix	169-171	3
β-strand	172-173	2	5
β-strand	179-188	10	5
α-helix	190-193	4
β-strand	198-203	6	6
α-helix	204-206	3
β-strand	208-213	6	6

Chain L: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	7
β-strand	5	1	8
β-strand	9-12	4	9
β-strand	18-23	6	8
β-strand	34-40	7	9
α-helix	45-46	2
β-strand	47-50	4	9
β-strand	51	1	10
β-strand	55	1	10
β-strand	64-69	6	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	86-93	8	9
β-strand	99-101	3	9
β-strand	102	1	7
β-strand	105-109	5	9
α-helix	112-114	3
β-strand	115	1	11
α-helix	116-117	2
β-strand	118-122	5	12
α-helix	126-130	5
β-strand	134-143	10	12
β-strand	144	1	11
β-strand	149-154	6	13
β-strand	157-159	3	13
β-strand	163-165	3	12
α-helix	166-168	3
β-strand	169-170	2	12
β-strand	176-184	9	12
α-helix	186-190	5
β-strand	195-201	7	13
β-strand	204-210	7	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DX-2507 Fab heavy chain	H	protein	219	Homo sapiens	S6BAN1 (AlphaFold model)
DX-2507 Fab light chain	L	protein	216	Homo sapiens	Q6NS95 (AlphaFold model)
IgG receptor FcRn large subunit p51	A	protein	297	Homo sapiens	P55899 (AlphaFold model)
Beta-2-microglobulin	B	protein	119	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>5WHK_1 DX-2507 Fab heavy chain (chains H)
EVQLLESGGGLVQPGGSLRLSCAASGFTFSEYAMGWVRQAPGKGLEWVSSIGSSGGQTKY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARLAIGDSYWGQGTMVTVSSASTK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 2 (L), FASTA

>5WHK_2 DX-2507 Fab light chain (chains L)
QSALTQPASVSGSPGQSITISCTGTGSDVGSYNLVSWYQQHPGKAPKLMIYGDSQRPSGV
SNRFSGSKSGNTASLTISGLQAEDEADYYCASYAGSGIYVFGTGTKVTVLGQPKANPTVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (A), FASTA

>5WHK_3 IgG receptor FcRn large subunit p51 (chains A)
MGVPRPQPWALGLLLFLLPGSLGAESHLSLLYHLTAVSSPAPGTPAFWVSGWLGPQQYLS
YNSLRGEAEPCGAWVWENQVSWYWEKETTDLRIKEKLFLEAFKALGGKGPYTLQGLLGCE
LGPDNTSVPTAKFALNGEEFMNFDLKQGTWGGDWPEALAISQRWQQQDKAANKELTFLLF
SCPHRLREHLERGRGNLEWKEPPSMRLKARPSSPGFSVLTCSAFSFYPPELQLRFLRNGL
AAGTGQGDFGPNSDGSFHASSSLTVKSGDEHHYCCIVQHAGLAQPLRVELESPAKSS

Sequence of entity 4 (B), FASTA

>5WHK_4 Beta-2-microglobulin (chains B)
MSRSVALAVLALLSLSGLEAIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLL
KNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
NHE	2-[N-cyclohexylamino]ethane sulfonic acid	C8 H17 N O3 S	2

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

Primary citation

Structural basis for pH-insensitive inhibition of immunoglobulin G recycling by an anti-neonatal Fc receptor antibody. Kenniston, J.A., Taylor, B.M., Conley, G.P. et al. J Biol Chem (2017) 292:17449-17460. DOI 10.1074/jbc.M117.807396 · PubMed

Other PDB entries of the same protein (UniProt S6BAN1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WHJ 2.15 Å, Crystal structure of Fab fragment of anti-FcRn antibody DX-2507

Browse structure collections

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