5VXR: The antigen-binding fragment of MAb24

The antigen-binding fragment of MAb24 in complex with a peptide from Hepatitis C Virus E2 epitope I (412-423). Determined by X-ray diffraction at 1.4 Å resolution. Released 21 Feb 2018.

Method: X-ray diffraction
Resolution: 1.4 Å
Organisms: Mus musculus, Hepatitis C virus
Chains: 3
Atoms: 3,870
Mol. weight: 49.46 kDa
Released: 21 Feb 2018

Explore 5VXR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VXR contains 12 α-helices and 46 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 H: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
β-strand	33-39	7	3
β-strand	45-52	8	3
β-strand	57-59	3	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	87-89	3
β-strand	91-98	8	3
β-strand	106-109	4	3
β-strand	113-115	3	3
β-strand	116-117	2	2
α-helix	121-122	2
β-strand	123	1	4
α-helix	124-125	2
β-strand	126-130	5	5
β-strand	141-151	11	5
β-strand	152	1	4
β-strand	157-159	3	6
β-strand	169-177	9	5
β-strand	180-190	11	5
β-strand	200-205	6	6
α-helix	206-208	3
β-strand	210-215	6	6
α-helix	216	1

Chain L: 7 helices, 23 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	27C-27D	2	9
β-strand	30-31	2	9
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	84-90	7	8
α-helix	96	1
β-strand	97-98	2	8
β-strand	102-106	5	8
β-strand	111	1	10
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	145-150	6	12
β-strand	153-155	3	12
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

Chain P: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	414-416	3	13
β-strand	419-421	3	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MAb24 Variable Heavy Chain,MAb24 Variable Heavy Chain	H	protein	217	Mus musculus	Q569X1 (AlphaFold model)
MAb24 Variable Light Chain,MAb24 Variable Light Chain	L	protein	217	Mus musculus	A0A125T908 (AlphaFold model)
Virus Envelope Protein 2	P	protein	12	Hepatitis C virus	Q5EG65

Sequence of entity 1 (H), FASTA

>5VXR_1 MAb24 Variable Heavy Chain,MAb24 Variable Heavy Chain (chains H)
VQLQESGPSLVKPSQTLSLTCSVTGDSITSGYWNWIRKFPGNKLEYVGYISYSGDTYYNP
SLKSRISITRDTSKNQYYLQLNSVTSEDTATYYCARMGYGSQPGFGSWGQGTLVTVSAAK
TTPPSVYPLAPGSGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLY
TMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEP

Sequence of entity 2 (L), FASTA

>5VXR_2 MAb24 Variable Light Chain,MAb24 Variable Light Chain (chains L)
NIVLTQSPVSLAVSLGQRATISCRASESVDSYGKSFLHWYQQKPGQPPKLLIYLASNLES
GVPARFSGSGSRTDFTLTIDPVEADDAATYYCQHNNEDPWTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERNNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRND

Sequence of entity 3 (P), FASTA

>5VXR_3 Virus Envelope Protein 2 (chains P)
QLINTNGSWHVN

Primary citation

Escape of Hepatitis C Virus from Epitope I Neutralization Increases Sensitivity of Other Neutralization Epitopes. Gu, J., Hardy, J., Boo, I. et al. J Virol (2018) 92. DOI 10.1128/JVI.02066-17 · PubMed

Other PDB entries of the same protein (UniProt Q569X1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5IKC 2.06 Å, X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN in complex with FAB
6U2F 2.94 Å, PCSK9-Fab 7G7 complex bound to cis-1-amino-4-phenylcyclohexaneacyl-WNLK(hR)IGLLR - NH2

Browse structure collections

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