3KR3: IGF-II antibody complex

Crystal structure of IGF-II antibody complex. Determined by X-ray diffraction at 2.2 Å resolution. Released 16 Jun 2010.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,004
Mol. weight: 57.9 kDa
Released: 16 Jun 2010

Explore 3KR3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3KR3 contains 23 α-helices and 45 β-strands across 3 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 D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
β-strand	26	1	1
α-helix	31-34	4
α-helix	37-44	8
α-helix	45-49	5
α-helix	53-58	6
β-strand	60	1	1

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	2
β-strand	10-12	3	3
β-strand	18-25	8	2
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	58-60	3	3
α-helix	62-64	3
β-strand	68-73	6	2
β-strand	78-83	6	2
α-helix	88-90	3
β-strand	92-99	8	3
β-strand	109-112	4	3
β-strand	116-120	5	3
α-helix	124-125	2
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
α-helix	164-166	3
β-strand	168	1	6
β-strand	172-174	3	5
α-helix	175-177	3
β-strand	178-179	2	5
β-strand	185-194	10	5
β-strand	204-209	6	6
α-helix	210-212	3
β-strand	214-219	6	6

Chain L: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	5-8	4	7
β-strand	11-15	5	8
β-strand	20-26	7	7
β-strand	34-39	6	8
β-strand	46-50	5	8
β-strand	54-55	2	8
α-helix	56	1
β-strand	63-67	5	7
β-strand	72-76	5	7
α-helix	81-83	3
β-strand	85-91	7	8
α-helix	98	1
β-strand	99	1	8
α-helix	100	1
β-strand	103-108	6	8
β-strand	112	1	9
α-helix	113-114	2
β-strand	115-119	5	10
α-helix	120-122	3
α-helix	123-127	5
β-strand	130-140	11	10
β-strand	141	1	9
β-strand	146-151	6	11
β-strand	154-155	2	11
α-helix	156	1
β-strand	160-164	5	10
β-strand	174-183	10	10
α-helix	184-188	5
β-strand	192-198	7	11
β-strand	206-211	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Insulin-like growth factor II	D	protein	67	Homo sapiens	P01344 (AlphaFold model)
antibody-Fab (heavy chain)	H	protein	251	Homo sapiens
antibody-Fab (light chain)	L	protein	215	Homo sapiens

Sequence of entity 1 (D), FASTA

>3KR3_1 Insulin-like growth factor II (chains D)
AYRPSETLCGGELVDTLQFVCGDRGFYFSRPASRVSRRSRGIVEECCFRSCDLALLETYC
ATPAKSE

Sequence of entity 2 (H), FASTA

>3KR3_2 antibody-Fab (heavy chain) (chains H)
EVQLLESGGGLVQPGGSLRLSCAASGFTFSNYIMWWVRQAPGKGLEWVSVISSSGGMTRY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDNGDYVGEKGFDIWGQGTMVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCAAAHHHHHHGAAEQK
LISEEDLNGAA

Sequence of entity 3 (L), FASTA

>3KR3_3 antibody-Fab (light chain) (chains L)
QDIQMTQSPSSLSASVGDRVTITCRASQSISNYLNWYQQKPGKAPKLLIYTASTLQSGVP
SRFSGSASGTDFTLTINSLQPEDFATYSCQQSYNSPWTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTQEDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

A human monoclonal antibody against insulin-like growth factor-II blocks the growth of human hepatocellular carcinoma cell lines in vitro and in vivo. Dransfield, D.T., Cohen, E.H., Chang, Q. et al. Mol Cancer Ther (2010) 9:1809-1819. DOI 10.1158/1535-7163.MCT-09-1134 · PubMed

Other PDB entries of the same protein (UniProt P01344 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3E4Z 2.28 Å, Crystal structure of human insulin degrading enzyme in complex with insulin-like growth…
6VWG 3.21 Å, Head region of the open conformation of the human type 1 insulin-like growth factor…
8YSZ 3.38 Å, Cryo-EM structure of the complex IR with three IGF-II
8U4C 3.6 Å, Cryo-EM structure of long form insulin receptor (IR-B) with four IGF2 bound, symmetric…
8VJB 3.6 Å, Cryo-EM structure of short form insulin receptor (IR-A) with four IGF2 bound, symmetric…
6VWI 3.7 Å, Head region of the closed conformation of the human type 1 insulin-like growth factor…
8VJC 3.8 Å, Cryo-EM structure of short form insulin receptor (IR-A) with three IGF2 bound,…
2V5P 4.1 Å, Complex structure of human IGF2R domains 11-13 bound to igf-II
8U4E 4.2 Å, Cryo-EM structure of long form insulin receptor (IR-B) with three IGF2 bound, asymmetric…
6UM2 4.32 Å, Structure of M-6-P/IGFII Receptor and IGFII complex
1IGL Solution structure of human insulin-like growth factor II relationship to receptor and…
2L29 Complex structure of E4 mutant human IGF2R domain 11 bound to IGF-II

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