Details

Structure visualisation

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Entry information

Complex
AACDB_ID:	6592
PDBID:	2R6P
Chains:	DE_A
Organism:	Dengue virus 2 Puerto Rico/PR159-S1/1969, Mus musculus
Method:	EM
Resolution (Å):	24.00
Reference:	10.1038/nsmb.1382
Antibody
Antibody:	1A1D-2 Fab
Antibody mutation:	No
INN (Clinical Trial):
Antigen
Antigen:	Dengue virus (DENV) 2 envelope glycoprotein
Antigen mutation:	No
Durg Target:	P27914; P12823;

Sequence information

Antibody

Heavy Chain: D
Mutation: NULL

>2R6P_D|Chain D, F|Heavy chain of 1A1D-2|Mus musculus (10090)
EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGYSKYDPKFQGKATITADTSSNAAYLQLSSLTSEDTAVYFCARDYEGFAYWGQGTLVTVSSAKTTPPSVYPLAPGAAAATSSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQTITCNVAHPASSTKVDKKIEPR

Light Chain: E
Mutation: NULL

>2R6P_E|Chain E, G|Light chain of 1A1D-2|Mus musculus (10090)
DIVLTQSPASLAVSLGQRATISCRASESVVRYGNSFMHWYQQKPGQPPKLLIYRASSLESGIPTRFSGSGSRTDFTLTINPVEADDVATYYCQQTNVDPWAFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDRQNGVLNSWTDQDSTYSMSSTLTLTKDEYERHNSYTCEATSPIVKSFNRNE

Antigen

Chain: A
Mutation: NULL

>2R6P_A|Chain A, B, C|Major envelope protein E|Dengue virus 2 Puerto Rico/PR159-S1/1969 (11066)
MRCIGISNRDFVEGVSSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTDSRCPTQGEPTLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFTCKKNMEGKIVQPENLEYTVVITPHSGEEHAVGNDTGKHGKEVKITPQSSITEAELTGYGTVTMECSPRTGLDFNEMVLLQMKDKAWLVHRQWFLDLPLPWLPGAGSNWIQKETLVTFKNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKG

Interaction

1、Solvent accessible surface areas (SASA) were calculated (Naccess V2.1.1) for each residue in antibody and antigen, respectively. The residues with SASA loss in binding of more than 1Å² were classified as interacting residues.

Interacting residues (ΔSASA based)

D: PHE27 THR32 ASP99 TYR100

E: TYR32 GLY33 SER57 SER60

A: VAL309 LYS310 GLU327 ASP362 GLY385 LEU389 ASN390

2、We defined interacting paratope-epitope residues by a distance cutoff of < 5Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 5 Å from any atom.

Interacting residues (Atom distance based)

Within the threshold, the structure has no interacting amino acids and cannot be displayed. This may be due to the following reasons:
1. The method used to determine the structure is electron microscopy or nuclear magnetic resonance, which results in too low resolution;
2. the coordinates of some amino acids involved in the interaction in the structure were not detected due to technical limitations. The results are less based on atomic coordinates, but the antibody does target the antigen.

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