3B2V: IMC-11F8 FAB Light chain

Crystal structure of the extracellular region of the epidermal growth factor receptor in complex with the Fab fragment of IMC-11F8. Determined by X-ray diffraction at 3.3 Å resolution. Released 19 Feb 2008.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,645
Mol. weight: 117.73 kDa
Ligands: NAG
Released: 19 Feb 2008

Explore 3B2V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3B2V contains 14 α-helices and 84 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 A: 8 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	261	1	19
β-strand	268	1	19
β-strand	277-278	2	20
α-helix	296-298	3
β-strand	301-302	2	20
β-strand	312-313	2	21
α-helix	332-335	4
β-strand	340-341	2	21
β-strand	345-347	3	22
β-strand	355	1	23
β-strand	360	1	23
α-helix	361-363	3
α-helix	366-368	3
β-strand	376-377	2	21
β-strand	381-383	3	22
β-strand	401-402	2	21
β-strand	414-416	3	22
β-strand	431-432	2	21
β-strand	437-440	4	22
α-helix	453-456	4
β-strand	457	1	21
β-strand	464-467	4	22
β-strand	469-470	2	6
α-helix	474-478	5
α-helix	481-483	3
β-strand	486	1	24
β-strand	491	1	25
α-helix	496-498	3
β-strand	499	1	25
β-strand	502	1	24
β-strand	505-507	3	26
β-strand	510-512	3	26
β-strand	525-527	3	27
β-strand	530-532	3	27
β-strand	538	1	28
β-strand	558	1	28
β-strand	585	1	29
β-strand	595	1	29

Chain H: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	10
β-strand	7	1	11
β-strand	11-12	2	12
β-strand	17-23	7	11
β-strand	24-25	2	10
β-strand	35-40	6	13
β-strand	48-53	6	13
β-strand	59-61	3	13
α-helix	63-65	3
β-strand	69	1	11
β-strand	72	1	11
β-strand	79-85	7	11
α-helix	89-91	3
β-strand	93-100	8	13
β-strand	108-111	4	13
β-strand	115-117	3	13
β-strand	118-119	2	12
β-strand	125	1	14
β-strand	128-132	5	15
β-strand	145-153	9	15
β-strand	154	1	14
α-helix	157	1
β-strand	158	1	16
β-strand	171-173	3	15
β-strand	177	1	17
β-strand	184	1	15
β-strand	185	1	17
β-strand	186-191	6	15
β-strand	203	1	18
β-strand	208	1	16
β-strand	218	1	18

Chain L: 3 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	7	1	2
β-strand	10-13	4	3
β-strand	19-21	3	4
β-strand	22	1	2
β-strand	24	1	5
β-strand	25	1	1
β-strand	34-38	5	3
β-strand	46-49	4	3
β-strand	53	1	3
β-strand	62-63	2	4
β-strand	66-67	2	5
β-strand	70-71	2	5
β-strand	73-75	3	4
β-strand	84-87	4	3
β-strand	93-94	2	6
α-helix	96	1
β-strand	103-106	4	3
β-strand	114	1	7
β-strand	117-118	2	8
α-helix	122-125	4
β-strand	132-134	3	8
β-strand	137	1	7
β-strand	146-150	5	9
β-strand	159	1	8
α-helix	165-167	3
β-strand	177-179	3	8
β-strand	192-196	5	9
β-strand	206	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IMC-11F8 FAB Light chain	L	protein	213	Homo sapiens	Q6PJF2 (AlphaFold model)
IMC-11F8 FAB Heavy chain	H	protein	223	Homo sapiens	P01857 (AlphaFold model)
Epidermal growth factor receptor	A	protein	624	Homo sapiens	P00533 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>3B2V_1 IMC-11F8 FAB Light chain (chains L)
EIVMTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYYCHQYGSTPLTFGGGTKAEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGA

Sequence of entity 2 (H), FASTA

>3B2V_2 IMC-11F8 FAB Heavy chain (chains H)
QVQLQESGPGLVKPSQTLSLTCTVSGGSISSGDYYWSWIRQPPGKGLEWIGYIYYSGSTD
YNPSLKSRVTMSVDTSKNQFSLKVNSVTAADTAVYYCARVSIFGVGTFDYWGQGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Sequence of entity 3 (A), FASTA

>3B2V_3 Epidermal growth factor receptor (chains A)
LEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQE
VAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKELPMRNLQEIL
HGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDFQNHLGSCQKCDPSCPNGSCWGAGE
ENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGCTGPRESDCLVCRKFRDEATCKDTC
PPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYVVTDHGSCVRACGADSYEMEEDGVR
KCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHT
PPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLN
ITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQ
VCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCNLLEGEPREFVENSECIQCHPECLP
QAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNC
TYGCTGPGLEGCPTNGPKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Structural basis for EGF receptor inhibition by the therapeutic antibody IMC-11F8. Li, S., Kussie, P., Ferguson, K.M. Structure (2008) 16:216-227. DOI 10.1016/j.str.2007.11.009 · PubMed

Other PDB entries of the same protein (UniProt Q6PJF2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3EO0 1.75 Å, Structure of the Transforming Growth Factor-Beta Neutralizing Antibody GC-1008
8QH0 1.87 Å, Crystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194
1DN0 2.28 Å, Structure of the FAB fragment from a human IgM cold agglutinin
2AGJ 2.6 Å, Crystal Structure of a glycosylated Fab from an IgM cryoglobulin with properties of a…
8QH1 2.65 Å, Crystal structure of the SARS-CoV-2 RBD from the Omicron BA4 variant with the antibody…
1U6A 2.81 Å, Crystal Structure of the Broadly Neutralizing Anti-HIV Fab F105
1QLR 2.83 Å, Crystal structure of the FAB fragment of a human monoclonal IgM cold agglutinin
4YPG 3.0 Å, Structural Insights Into the Neutralization Properties of a Human Anti-Interferon…
3EO1 3.1 Å, Structure of the Fab Fragment of GC-1008 in Complex with Transforming Growth Factor-Beta 3
6MYY 3.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs…
6UDK 3.9 Å, HIV-1 bNAb 1-55 in complex with modified BG505 SOSIP-based immunogen RC1 and 10-1074
6MZJ 4.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 2 Fabs…

Browse structure collections

About this viewer

MolViewer shows 3B2V directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.