Structure summary for 3RKD

Detailed entry information.

Key:

Heavy Chains
Light Chains
Bound Antigen Chains
Chothia CDRs
Other

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Hepatitis E Virus E2S Domain (Genotype I) In Complex With A Neutralizing Antibody

ItemInfo
PDB code: 3rkd
Organism: MUS MUSCULUS
Experimental method: X-RAY DIFFRACTION
In complex: True
Fvs present: 2
Binding affinity (KD): 5.89e-09 M
ΔG: -11.22 kcal/mol
Affinity method: SPR
Source: Paper Link
Light chain type: Kappa
PDB has constant region: True

This PDB has 2 antibody variable fragment(s)

Fab Details:
ItemInfo
Heavy Chain D
Light Chain C
Heavy V / J / C subgroups IGHV8 / IGHJ4 / IGHG1
Light V / J / C subgroups IGKV12 / IGKJ1 / IGKC
Bound-state Bound
Species MUS MUSCULUS
ScFv? False
Constant domains present? True
Antigen Details:
ItemInfo
Chain B
Type protein
Name capsid protein
Species HEPATITIS E VIRUS

Sequence:
Chain typeChain idFasta sequenceChothia annotated sequence ( framework / CDRs )
VH D Download
H1 H2 H3 H4 H5 H6 H7 H8 H9 H10
QVTLKESGPG
H11 H12 H13 H14 H15 H16 H17 H18 H19 H20
ILQPSQTLSL
H21 H22 H23 H24 H25 H26 H27 H28 H29 H30
TCSFSGFSLS
H31 H31AH31BH32 H33 H34 H35 H36 H37 H38
TSGMGVGWIR
H39 H40 H41 H42 H43 H44 H45 H46 H47 H48
QPSGKGLEWL
H49 H50 H51 H52 H53 H54 H55 H56 H57 H58
AHIWWDDVKR
H59 H60 H61 H62 H63 H64 H65 H66 H67 H68
YSPALKSRLT
H69 H70 H71 H72 H73 H74 H75 H76 H77 H78
ISKDTSSSQL
H79 H80 H81 H82 H82AH82BH82CH83 H84 H85
FLKIASVDTA
H86 H87 H88 H89 H90 H91 H92 H93 H94 H95
DTATYYCARI
H96 H97 H98 H99 H100 H100AH100BH100CH100DH100E
KSVITTGDYA
H100FH101 H102 H103 H104 H105 H106 H107 H108 H109
LDYWGQGTSV
H110 H111 H112 H113
AVSS
VL C Download
L1 L2 L3 L4 L5 L6 L7 L8 L9 L10
DIQMTQSPAS
L11 L12 L13 L14 L15 L16 L17 L18 L19 L20
LSVSVGETVT
L21 L22 L23 L24 L25 L26 L27 L28 L29 L30
ITCRASEIIY
L31 L32 L33 L34 L35 L36 L37 L38 L39 L40
SNLAWYQQKQ
L41 L42 L43 L44 L45 L46 L47 L48 L49 L50
GKSPQLLVYS
L51 L52 L53 L54 L55 L56 L57 L58 L59 L60
ATNLAEGVPS
L61 L62 L63 L64 L65 L66 L67 L68 L69 L70
RFSGSGSGTQ
L71 L72 L73 L74 L75 L76 L77 L78 L79 L80
YSLKINSLQS
L81 L82 L83 L84 L85 L86 L87 L88 L89 L90
EDFGSYYCQH
L91 L92 L93 L94 L95 L96 L97 L98 L99 L100
FWGNPWTFGG
L101 L102 L103 L104 L105 L106 L107 L108 L109
GTKLEIKRA
Antigen typeChain idFasta sequenceSequence (Clustal colouring)
protein B Download
S R P F S V L R A N D V L W L S L T A A E Y D Q S T Y G S S
T G P V Y V S D S V T L V N V A T G A Q A V A R S L D W T K
V T L D G R P L S T I Q Q H S K T F F V L P L R G K L S F W
E A G T T K A G Y P Y N Y N T T A S D Q L L V E N A A G H R
V A I S T Y T T S L G A G P V S I S A V A V L A P P

Antibody i-Patch annotation:
Fab heavy/lightchainLink to the Antibody i-Patch annotation (What is this?)
D/CGet AB i-Patch annotation
Chothia CDR information:
CDRSequence
CDRL1 RASEIIYSNLA
CDRL2 SATNLAE
CDRL3 QHFWGNPWT
CDRH1 GFSLSTSGM
CDRH2 WWDDV
CDRH3 IKSVITTGDYALDY
VH-VL orientation:
(see plot)
AngleValue
HL -60.0°
HC1 70.7°
HC2 118.1°
LC1 119.6°
LC2 80.9°
dc 16.3 Å
Fab Details:
ItemInfo
Heavy Chain H
Light Chain L
Heavy V / J / C subgroups IGHV8 / IGHJ4 / IGHG1
Light V / J / C subgroups IGKV12 / IGKJ1 / IGKC
Bound-state Bound
Species MUS MUSCULUS
ScFv? False
Constant domains present? True
Antigen Details:
ItemInfo
Chain A
Type protein
Name capsid protein
Species HEPATITIS E VIRUS

Sequence:
Chain typeChain idFasta sequenceChothia annotated sequence ( framework / CDRs )
VH H Download
H1 H2 H3 H4 H5 H6 H7 H8 H9 H10
QVTLKESGPG
H11 H12 H13 H14 H15 H16 H17 H18 H19 H20
ILQPSQTLSL
H21 H22 H23 H24 H25 H26 H27 H28 H29 H30
TCSFSGFSLS
H31 H31AH31BH32 H33 H34 H35 H36 H37 H38
TSGMGVGWIR
H39 H40 H41 H42 H43 H44 H45 H46 H47 H48
QPSGKGLEWL
H49 H50 H51 H52 H53 H54 H55 H56 H57 H58
AHIWWDDVKR
H59 H60 H61 H62 H63 H64 H65 H66 H67 H68
YSPALKSRLT
H69 H70 H71 H72 H73 H74 H75 H76 H77 H78
ISKDTSSSQL
H79 H80 H81 H82 H82AH82BH82CH83 H84 H85
FLKIASVDTA
H86 H87 H88 H89 H90 H91 H92 H93 H94 H95
DTATYYCARI
H96 H97 H98 H99 H100 H100AH100BH100CH100DH100E
KSVITTGDYA
H100FH101 H102 H103 H104 H105 H106 H107 H108 H109
LDYWGQGTSV
H110 H111 H112 H113
AVSS
VL L Download
L1 L2 L3 L4 L5 L6 L7 L8 L9 L10
DIQMTQSPAS
L11 L12 L13 L14 L15 L16 L17 L18 L19 L20
LSVSVGETVT
L21 L22 L23 L24 L25 L26 L27 L28 L29 L30
ITCRASEIIY
L31 L32 L33 L34 L35 L36 L37 L38 L39 L40
SNLAWYQQKQ
L41 L42 L43 L44 L45 L46 L47 L48 L49 L50
GKSPQLLVYS
L51 L52 L53 L54 L55 L56 L57 L58 L59 L60
ATNLAEGVPS
L61 L62 L63 L64 L65 L66 L67 L68 L69 L70
RFSGSGSGTQ
L71 L72 L73 L74 L75 L76 L77 L78 L79 L80
YSLKINSLQS
L81 L82 L83 L84 L85 L86 L87 L88 L89 L90
EDFGSYYCQH
L91 L92 L93 L94 L95 L96 L97 L98 L99 L100
FWGNPWTFGG
L101 L102 L103 L104 L105 L106 L107 L108 L109
GTKLEIKRA
Antigen typeChain idFasta sequenceSequence (Clustal colouring)
protein A Download
S R P F S V L R A N D V L W L S L T A A E Y D Q S T Y G S S
T G P V Y V S D S V T L V N V A T G A Q A V A R S L D W T K
V T L D G R P L S T I Q Q H S K T F F V L P L R G K L S F W
E A G T T K A G Y P Y N Y N T T A S D Q L L V E N A A G H R
V A I S T Y T T S L G A G P V S I S A V A V L A P P

Antibody i-Patch annotation:
Fab heavy/lightchainLink to the Antibody i-Patch annotation (What is this?)
H/LGet AB i-Patch annotation
Chothia CDR information:
CDRSequence
CDRL1 RASEIIYSNLA
CDRL2 SATNLAE
CDRL3 QHFWGNPWT
CDRH1 GFSLSTSGM
CDRH2 WWDDV
CDRH3 IKSVITTGDYALDY
VH-VL orientation:
(see plot)
AngleValue
HL -59.0°
HC1 70.3°
HC2 118.8°
LC1 120.9°
LC2 81.6°
dc 16.2 Å

Downloads and links.

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Full structureDownload
Chothia structureDownload
Summary fileDownload
Entry in the PDBSee the file on the PDB
Entry in IMGTSee the IMGT entry
Flag misannotation