6KVF: Anti-hCXCR2 abN48

Structure of anti-hCXCR2 abN48 in complex with its CXCR2 epitope. Determined by X-ray diffraction at 2.79 Å resolution. Released 9 Sept 2020.

Method: X-ray diffraction
Resolution: 2.79 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,478
Mol. weight: 98 kDa
Released: 9 Sept 2020

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

Secondary structure: helices and β-sheets

6KVF contains 32 α-helices and 87 β-strands across 5 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: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	6
α-helix	8-10	3
β-strand	11-13	3	7
β-strand	19-25	7	6
β-strand	35-40	6	7
β-strand	46-52	7	7
β-strand	59-61	3	7
β-strand	69-74	6	6
β-strand	79-84	6	6
α-helix	89-91	3
β-strand	93-102	10	7
β-strand	106-111	6	7
β-strand	115-119	5	7
β-strand	125	1	8
α-helix	126-127	2
β-strand	128-132	5	9
β-strand	143-153	11	9
β-strand	154	1	8
β-strand	159-162	4	10
β-strand	171-173	3	9
α-helix	174-176	3
β-strand	177-178	2	9
β-strand	184-193	10	9
β-strand	203-208	6	10
α-helix	209-211	3
β-strand	213-218	6	10

Chain b: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	12-13	2	2

Chain C: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	15
β-strand	9-12	4	7
β-strand	18-24	7	15
α-helix	25	1
α-helix	30-32	3
α-helix	34	1
β-strand	35-40	6	7
β-strand	47-52	6	7
β-strand	58-61	4	7
β-strand	68-73	6	15
β-strand	78-83	6	15
α-helix	88-90	3
β-strand	92-100	9	7
β-strand	103-106	4	7
β-strand	110-114	5	7
β-strand	121	1	16
α-helix	122-123	2
β-strand	124-128	5	17
α-helix	129-131	3
α-helix	132-136	5
β-strand	140-149	10	17
β-strand	150	1	16
β-strand	155-160	6	18
β-strand	163-164	2	18
α-helix	165	1
β-strand	169-171	3	17
α-helix	172-174	3
β-strand	175-176	2	17
β-strand	182-190	9	17
α-helix	192-197	6
β-strand	201-207	7	18
β-strand	210-216	7	18

Chain H: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	1
α-helix	8-10	3
β-strand	11-13	3	2
β-strand	19-25	7	1
β-strand	35-40	6	2
β-strand	46-52	7	2
β-strand	59-61	3	2
β-strand	69-74	6	1
β-strand	79-84	6	1
α-helix	89-91	3
β-strand	93-102	10	2
β-strand	106-111	6	2
β-strand	115-119	5	2
α-helix	122-124	3
β-strand	125	1	3
β-strand	128-132	5	4
β-strand	143-153	11	4
β-strand	154	1	3
β-strand	158-162	5	5
β-strand	171-173	3	4
α-helix	174-176	3
β-strand	177-178	2	4
β-strand	184-193	10	4
α-helix	194-196	3
β-strand	203-208	6	5
α-helix	209-211	3
β-strand	213-218	6	5

Chain L: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	11
β-strand	9-12	4	2
β-strand	18-24	7	11
α-helix	25	1
α-helix	30-32	3
α-helix	34	1
β-strand	35-40	6	2
α-helix	45-46	2
β-strand	47-52	6	2
β-strand	58-61	4	2
β-strand	68-73	6	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	104-106	3	2
β-strand	110-114	5	2
α-helix	118-120	3
β-strand	121	1	12
α-helix	122-123	2
β-strand	124-128	5	13
α-helix	129-131	3
α-helix	132-136	5
β-strand	140-149	10	13
β-strand	150	1	12
β-strand	155-160	6	14
β-strand	163-165	3	14
β-strand	169-171	3	13
α-helix	172-174	3
β-strand	175-176	2	13
β-strand	182-190	9	13
α-helix	192-197	6
β-strand	201-207	7	14
β-strand	210-216	7	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
heavy chain	A, H	protein	227	Homo sapiens
light chain	C, L	protein	222	Homo sapiens
Peptide from C-X-C chemokine receptor type 2	B, b	protein	11	Homo sapiens	P25025 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>6KVF_1 heavy chain (chains A, H)
MQVQLVQSGAEVKKPGSSVKVSCKASGGTLSSYAISWVRQAPGQGPEWMGWINPNSGGTN
YAQKFQGRVTMTRDTSISTAYMELSRLRPDDTAVYYCASGYCSSTSCYDYWGQGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPPKSCDK

Sequence of entity 2 (C, L), FASTA

>6KVF_2 light chain (chains C, L)
QAVLTQPSSLSASPGASVSLTCTLRSGINVGAYRIYWYQQKPGSPPQFLLRYKSDSDKQQ
GSGVPSRFSGSRDASANAGILLISGLRSEDEADYYCAIWHSSAWVFGGGTQLTVLGGQPK
AAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNN
KYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (B, b), FASTA

>6KVF_3 Peptide from C-X-C chemokine receptor type 2 (chains B, b)
DSFEDFWKGED

Primary citation

Selection of a picomolar antibody that targets CXCR2-mediated neutrophil activation and alleviates EAE symptoms. Shi, X., Wan, Y., Wang, N. et al. Nat Commun (2021) 12:2547-2547. DOI 10.1038/s41467-021-22810-z · PubMed

Other PDB entries of the same protein (UniProt P25025 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KVA 2.2 Å, Structure of anti-hCXCR2 abN48-2 in complex with its CXCR2 epitope
8XXH 2.8 Å, Structure of CXCR2 bound to CXCL2 (CXCR2-CXCL2-Go Full map)
8XX6 2.99 Å, Structure of CXCR2 bound to CXCL8 (CXCR2-CXCL8-Go Full map)
8XWS 3.06 Å, Structure of CXCR2 bound to CXCL5 (Ligand-receptor focused map)
8XWV 3.07 Å, Structure of CXCR2 bound to CXCL1 (CXCR2-CXCL1-Go Full map)
8XVU 3.09 Å, Structure of CXCR2 bound to CXCL2 (Ligand-receptor focused map)
8XXR 3.17 Å, Structure of CXCR2 bound to CXCL6 (CXCR2-CXCL6-Go Full map)
8XXX 3.17 Å, Structure of CXCR2 bound to CXCL6 (Composite map)
6LFL 3.2 Å, Crystal structure of a class A GPCR
8XWN 3.29 Å, Structure of CXCR2 bound to CXCL8 (Ligand-receptor focused map)
8XX7 3.32 Å, Structure of CXCR2 bound to CXCL5 (CXCR2-CXCL5-Go Full map)
8XX3 3.38 Å, Structure of CXCR2 bound to CXCL3 (CXCR2-CXCL3-Go Full map)

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