6WZM: LY3041658 Fab

LY3041658 Fab bound to CXCL8. Determined by X-ray diffraction at 2.28 Å resolution. Released 25 Nov 2020.

Method: X-ray diffraction
Resolution: 2.28 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,171
Mol. weight: 111.06 kDa
Released: 25 Nov 2020

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

Secondary structure: helices and β-sheets

6WZM contains 31 α-helices and 96 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 C: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	33-39	7	2
β-strand	46-51	6	2
β-strand	58-60	3	2
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	113-116	4	2
β-strand	120-124	5	2
β-strand	130	1	3
β-strand	133-137	5	4
β-strand	148-158	11	4
β-strand	159	1	3
β-strand	164-167	4	5
α-helix	168-170	3
β-strand	172	1	5
β-strand	176-178	3	4
α-helix	179-181	3
β-strand	182-183	2	4
β-strand	189-198	10	4
β-strand	208-213	6	5
α-helix	214-216	3
β-strand	218-223	6	5

Chain B: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	29	1	8
β-strand	31	1	8
β-strand	33-38	6	7
β-strand	45-49	5	7
β-strand	53-54	2	7
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-90	6	7
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-106	5	7
β-strand	111	1	9
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-154	2	11
α-helix	155	1
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-187	5
β-strand	191-197	7	11
β-strand	205-210	6	11

Chain D: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-13	4	18
β-strand	19-25	7	17
β-strand	29	1	19
β-strand	31	1	19
β-strand	33-38	6	18
β-strand	45-49	5	18
β-strand	53-54	2	18
β-strand	62-67	6	17
β-strand	70-75	6	17
α-helix	80-82	3
β-strand	85-90	6	18
α-helix	96	1
β-strand	97-98	2	18
β-strand	102-106	5	18
β-strand	111	1	20
α-helix	112-113	2
β-strand	114-118	5	21
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	21
β-strand	140	1	20
β-strand	145-150	6	22
β-strand	153-154	2	22
α-helix	155	1
β-strand	159-163	5	21
α-helix	164-167	4
β-strand	173-182	10	21
α-helix	183-187	5
β-strand	191-197	7	22
β-strand	205-210	6	22

Chains E and F: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
β-strand	22-28	7	23
β-strand	38-43	6	23
β-strand	48-51	4	23
α-helix	56-63	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
LY3041658 Fab heavy chain	A, C	protein	224	Homo sapiens
LY3041658 Fab light chain	B, D	protein	214	Homo sapiens
Interleukin-8	E, F	protein	66	Homo sapiens	P10145 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6WZM_1 LY3041658 Fab heavy chain (chains A, C)
QVQLVQSGAEVKKPGASVKVSCKASGYEFTSYWIHWVRQAPGQGLEWMGNISPNSGSANY
NEKFKSRVTMTRDTSTSTVYMELSSLRSEDTAVYYCAREGPYSYYPSREYYGSDLWGQGT
LVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRV

Sequence of entity 2 (B, D), FASTA

>6WZM_2 LY3041658 Fab light chain (chains B, D)
EIVLTQSPATLSLSPGERATLSCRASQSISNNLHWYQQKPGQAPRLLIYYTSRSVSGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYYCGQNNEWPEVFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (E, F), FASTA

>6WZM_3 Interleukin-8 (chains E, F)
SAKELRCQCIKTYSKPFHPKFIKELRVIESGPHCANTEIIVKLSDGRELCLDPKENWVQR
VVEKFL

Primary citation

Discovery and characterization of a neutralizing pan-ELR+CXC chemokine monoclonal antibody. Boyles, J.S., Beidler, C.B., Strifler, B.A. et al. MAbs 12:1831880-1831880. DOI 10.1080/19420862.2020.1831880 · PubMed

Other PDB entries of the same protein (UniProt P10145 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4XDX 0.95 Å, The crystal structure of soluble human interleukin 8 expressed in Pichia pastoris
5D14 1.0 Å, The atomic resolution crystal structure of human IL-8
6N2U 1.25 Å, IL-8 Structure from Bacterial Expression Source
3IL8 2.0 Å, Crystal structure of interleukin 8: symbiosis of NMR and crystallography
1ICW 2.01 Å, Interleukin-8, mutant with glu 38 replaced by cys and cys 50 replaced by ala
9YIP 2.2 Å, Crystal structure of human IL-8 in a large unit cell
1QE6 2.35 Å, Interleukin-8 with an added disulfide between residues 5 and 33 (L5C/H33C)
8XX6 2.99 Å, Structure of CXCR2 bound to CXCL8 (CXCR2-CXCL8-Go Full map)
8XWN 3.29 Å, Structure of CXCR2 bound to CXCL8 (Ligand-receptor focused map)
6LFO 3.4 Å, Cryo-EM structure of a class A GPCR monomer
8IC0 3.41 Å, Cryo-EM structure of CXCL8 bound C-X-C chemokine receptor 1 in complex with Gi…
6LFM 3.5 Å, Cryo-EM structure of a class A GPCR

Browse structure collections

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