Structure Viewer: 6utk

>   Structure details

Crystal Structure of 438-B11 Fab in complex with an Uncleaved Prefusion Optimized (Ufo) Soluble Bg505 Trimer and Fab 35O22 at 3.80 angstrom

PDB6utk
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution3.8Å
Number of Fvs2
In complexTrue
Light chain typeKappa,unknown
Has constant regionTrue
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>   Fv information

This PDB has 2 Fv(s).

>   D/E
Fv Details
Heavy chainD
Light chainE
Heavy subgroupunknown
Light subgroupunknown
SpeciesHOMO SAPIENS
In complex?True
scFv?False
Has constant domain?True

Numbered Sequences (chothia)

Heavy chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 52A 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 73A 73B 73C 73D 73E 73F 73G 73H 74 75 76 77 78 79 80 81 82 82A 82B 82C 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 100A 100B 100C 100D 100E 100F 101 102 103 104 105 106 107 108 109 110 111 112 113
E G Q L V Q S G A E L K K P G A S V K I S C K T S G Y R F N F Y H I N W I R Q T A G R G P E W M G W I S P Y S G D K N L A P A F Q D R V I M T T D T E V P V T S F T S T G A A Y M E I R N L K F D D T G T Y F C A K G L L R D G S S T W L P Y L W G Q G T L L T V S S

Light chain

1 2 3 4 5 6 7 8 9 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 30A 30B 30C 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 95A 96 97 98 99 100 101 102 103 104 105 106 107
Q S V L T Q S A S V S G S L G Q S V T I S C T G P N S V C C S H K S I S W Y Q W P P G R A P T L I I Y E D N E R A P G I S P R F S G Y K S Y W S A Y L T I S D L R P E D E T T Y Y C C S Y T H N S G C V F G T G T K V S V L

Antigen Details
Antigen chainsT
Antigen typeprotein
Antigen nameenvelope glycoprotein gp41
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGNPDWLPDMTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

CDR Sequences (chothia definition)
CDRH1GYRFNFY
CDRH2SPYSGD
CDRH3GLLRDGSSTWLPYL
CDRL1TGPNSVCCSHKSIS
CDRL2EDNERAP
CDRL3CSYTHNSGCV

Orientation Angles (from ABangle)
HL-60.73°
HC173.3°
HC2123.11°
LC1123.31°
LC286.84°
dc16.17Å
>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupunknown
Light subgroupIGKV3
SpeciesHOMO SAPIENS
In complex?True
scFv?False
Has constant domain?True

Numbered Sequences (chothia)

Heavy chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 52A 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 82A 82B 82C 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 100A 100B 100C 100D 100E 100F 100G 100H 100I 100J 100K 100L 100M 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L V Q S G A E V R K P G S S V T I S C K P V G G T F T N F A I H W V R Q A P G Q G L E W V G G R V P V V G I Y K Y G K K F H D R L R L Y E D D P M K T V F L E L R S L T S D D T G V Y Y C T R W R G C G M C P Y D T S S Y Y N D A S D V W G P G T K V I V S A

Light chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 30A 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107
E I V L T Q S P V T L S L S S G E T G T L S C R A S Q N I S S S W I A W Y Q Q R R G Q V P R L L I S A A S A R A A G I P D R F T G R G S G T D F T L T I T R L E P E D F G V Y S C Q Y Y G G S F F T F G P G T Q V D V K

Antigen Details
Antigen chainsG
Antigen typeprotein
Antigen nameenvelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAENLWVTVYYGVPVWKDAETTLFCASDAKAYDTEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGGGGGSGGGGS

CDR Sequences (chothia definition)
CDRH1GGTFTNF
CDRH2VPVVGI
CDRH3WRGCGMCPYDTSSYYNDASDV
CDRL1RASQNISSSWIA
CDRL2AASARAA
CDRL3QYYGGSFFT

Orientation Angles (from ABangle)
HL-57.54°
HC173.23°
HC2119.23°
LC1120.68°
LC283.88°
dc15.9Å
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Additional links and files for download: see help for more details.

Chothia-numbered structure Download
IMGT-numbered structure Download
Non-annotated structure from the PDB Download
Summary file for this antibody Download

Schneider, C., Raybould, M.I.J., Deane, C.M. (2022) SAbDab in the Age of Biotherapeutics: Updates including SAbDab-Nano, the Nanobody Structure Tracker. Nucleic Acids Res. 50(D1):D1368-D1372 [link]

SAbDab paper: Dunbar, J., Krawczyk, K. et al (2014). Nucleic Acids Res. 42. D1140-D1146 [link]

Thera-SAbDab paper: Raybould, M.I.J., Marks, C. et al (2019). Nucleic Acids Res. gkz827 [link]

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