4CNI: Fab portion of Olokizumab

Crystal structure of the Fab portion of Olokizumab in complex with IL- 6. Determined by X-ray diffraction at 2.2 Å resolution. Released 30 Apr 2014.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: HOMO SAPIENS
Chains: 6
Atoms: 10,999
Mol. weight: 134.59 kDa
Ligands: TAM
Released: 30 Apr 2014

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

Secondary structure: helices and β-sheets

4CNI contains 61 α-helices and 92 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: 12 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
α-helix	54-56	3
β-strand	60-62	3	2
α-helix	64-66	3
β-strand	70-75	6	1
α-helix	76-78	3
β-strand	80-85	6	1
α-helix	90-92	3
β-strand	94-101	8	2
α-helix	102	1
β-strand	107-110	4	2
β-strand	114-118	5	2
α-helix	121-123	3
β-strand	124	1	3
α-helix	125-126	2
β-strand	127-131	5	4
β-strand	142-152	11	4
β-strand	153	1	3
β-strand	158-161	4	5
α-helix	162-164	3
β-strand	166	1	5
β-strand	170-172	3	4
α-helix	173-175	3
β-strand	176-177	2	4
β-strand	183-192	10	4
α-helix	193-195	3
β-strand	196	1	6
β-strand	199	1	6
β-strand	201-207	7	5
α-helix	208-210	3
β-strand	212-218	7	5

Chain B: 10 helices, 22 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	93	1	9
α-helix	96	1
β-strand	97-98	2	8
β-strand	102-106	5	8
β-strand	111	1	10
α-helix	112-113	2
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	145-150	6	12
β-strand	153-154	2	12
α-helix	155	1
β-strand	159-163	5	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-187	5
β-strand	191-197	7	12
β-strand	205-210	6	12
α-helix	211-213	3

Chain C: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	21-43	23
α-helix	56-59	4
α-helix	69-71	3
α-helix	80-104	25
α-helix	109-129	21
α-helix	134-140	7
α-helix	141-153	13
β-strand	154	1	13
α-helix	156-181	26

Chain D: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	21-44	24
α-helix	56-59	4
α-helix	69-71	3
α-helix	80-104	25
α-helix	109-130	22
α-helix	138-140	3
α-helix	141-153	13
β-strand	154	1	9
α-helix	156-181	26

Chain H: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	10-12	3	15
β-strand	18-25	8	14
α-helix	29-31	3
β-strand	34-39	6	15
β-strand	45-51	7	15
α-helix	54-56	3
β-strand	60-62	3	15
α-helix	64-66	3
β-strand	70-75	6	14
α-helix	76-78	3
β-strand	80-85	6	14
α-helix	90-92	3
β-strand	94-101	8	15
α-helix	102	1
β-strand	107-110	4	15
β-strand	114-118	5	15
α-helix	121-123	3
β-strand	124	1	16
α-helix	125-126	2
β-strand	127-131	5	17
β-strand	142-152	11	17
β-strand	153	1	16
β-strand	158-161	4	18
α-helix	162-164	3
β-strand	166	1	18
β-strand	170-172	3	17
α-helix	173-175	3
β-strand	176-177	2	17
β-strand	183-192	10	17
α-helix	193-195	3
β-strand	202-207	6	18
α-helix	208-210	3
β-strand	212-217	6	18

Chain L: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	10-13	4	20
β-strand	19-25	7	19
β-strand	33-38	6	20
β-strand	45-49	5	20
β-strand	53-54	2	20
α-helix	55	1
β-strand	62-67	6	19
β-strand	70-75	6	19
α-helix	80-82	3
β-strand	85-90	6	20
β-strand	93	1	13
α-helix	96	1
β-strand	97-98	2	20
β-strand	102-106	5	20
β-strand	111	1	21
α-helix	112-113	2
β-strand	114-118	5	22
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	22
β-strand	140	1	21
β-strand	145-150	6	23
β-strand	153-154	2	23
α-helix	155	1
β-strand	159-163	5	22
α-helix	164-167	4
β-strand	173-182	10	22
α-helix	183-186	4
β-strand	191-197	7	23
β-strand	205-210	6	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Olokizumab heavy chain, FAB portion	A, H	protein	220	HOMO SAPIENS
Olokizumab light chain, FAB portion	B, L	protein	214	HOMO SAPIENS
Interleukin-6	C, D	protein	171	HOMO SAPIENS	P05231 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>4CNI_1 OLOKIZUMAB HEAVY CHAIN, FAB PORTION (chains A, H)
EVQLVESGGGLVQPGGSLRLSCAASGFNFNDYFMNWVRQAPGKGLEWVAQMRNKNYQYGT
YYAESLEGRFTISRDDSKNSLYLQMNSLKTEDTAVYYCARESYYGFTSYWGQGTLVTVSS
ASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVES

Sequence of entity 2 (B, L), FASTA

>4CNI_2 OLOKIZUMAB LIGHT CHAIN, FAB PORTION (chains B, L)
DIQMTQSPSSLSASVGDRVTITCQASQDIGISLSWYQQKPGKAPKLLIYNANNLADGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCLQHNSAPYTFGQGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, D), FASTA

>4CNI_3 INTERLEUKIN-6 (chains C, D)
PHRQPLTSSERIDKQIRYILDGISALRKETCNKSNMCESSKEALAENNLNLPKMAEKDGC
FQSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMSTKVLIQFLQKKAKNL
DAITTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSLRALRQM

Ligands and cofactors

ID	Name	Formula	Copies
TAM	Tris(hydroxyethyl)aminomethane	C7 H17 N O3	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Discovery and Characterization of Olokizumab: A Humanized Antibody Targeting Interleukin-6 and Neutralizing Gp130-Signaling. Shaw, S., Bourne, T., Meier, C. et al. MAbs (2014) 6:773. DOI 10.4161/MABS.28612 · PubMed

Other PDB entries of the same protein (UniProt P05231 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1ALU 1.9 Å, Human interleukin-6
7NXZ 2.0 Å, Synthetic glycoform of Human Interleukin 6
4J4L 2.3 Å, Modular evolution and design of the protein binding interface
4NI7 2.4 Å, Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer…
4O9H 2.42 Å, Structure of Interleukin-6 in complex with a Camelid Fab fragment
8YWQ 2.51 Å, Crystal structure of the Fab fragment of the anti-IL-6 antibody I9H in complex with a…
4NI9 2.55 Å, Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer…
5FUC 2.7 Å, Biophysical and cellular characterisation of a junctional epitope antibody that locks…
4ZS7 2.93 Å, Structural mimicry of receptor interaction by antagonistic IL-6 antibodies
8YWR 2.93 Å, Crystal structure of the Fab fragment of the anti-IL-6 antibody 68F2 in complex with a…
8QY5 3.1 Å, Structure of interleukin 6.
8QY6 3.16 Å, Structure of interleukin 6 (gp130 P496L mutant).

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