Structure Viewer: 7cn2

>   Structure details

Subparticle Refinement of Human Papillomavirus Type 16 Pesudovirus in complex with H16.001 Fab

PDB7cn2
SpeciesORYCTOLAGUS CUNICULUS
MethodELECTRON MICROSCOPY
Resolution3.43Å
Number of Fvs6
In complexTrue
Light chain typeKappa
Has constant regionFalse
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>   Fv information

This PDB has 6 Fv(s).

>   G/g
Fv Details
Heavy chainG
Light chaing
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesORYCTOLAGUS CUNICULUS
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 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 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
Q S V K E S E G R L V T P G T P L T L T C T A S G F T M S R Y H M T W V R Q A P G K G L E W I G I I Y A R N S D T Y Y A N W A K G R F T I S K T S T T V D L K I T S P T I E D T A T Y F C A R V D S D S S G A F D R L D L W G Q G T L V T V S S

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 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 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
D P M L T Q T A A S V E V A V G G T V T I K C Q A S Q S I G G Y L S W Y Q Q K P G Q R P K L L I Y R A S T L A S G V P S R F K G S G S G T E Y T L T F S G V E C A D A A A Y Y C Q Q G Y T S S D I N N A F G G G T E V V V K

Antigen Details
Antigen chainsE
Antigen typeprotein
Antigen namemajor capsid protein l1
Antigen speciesHUMAN PAPILLOMAVIRUS TYPE 16
Antigen sequenceMSLWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYRVFRIHLPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGISGHPLLNKLDDTENASAYAANAGVDNRECISMDYKQTQLCLIGCKPPIGEHWGKGSPCTNVAVNPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSICKYPDYIKMVSEPYGDSLFFYLRREQMFVRHLFNRAGAVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMVTSDAQIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNFKEYLRHGEEYDLQFIFQLCKITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVTSQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFSADLDQFPLGRKFLLQAGLKAKPKFTLGKRKATPTTSSTSTTAKRKKRKL

CDR Sequences (chothia definition)
CDRH1GFTMSRY
CDRH2YARNSD
CDRH3VDSDSSGAFDRLDL
CDRL1QASQSIGGYLS
CDRL2RASTLAS
CDRL3QQGYTSSDINNA

Orientation Angles (from ABangle)
HL-51.8°
HC170.78°
HC2119.18°
LC1122.0°
LC286.23°
dc16.97Å
>   I/i
Fv Details
Heavy chainI
Light chaini
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesORYCTOLAGUS CUNICULUS
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 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 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
Q S V K E S E G R L V T P G T P L T L T C T A S G F T M S R Y H M T W V R Q A P G K G L E W I G I I Y A R N S D T Y Y A N W A K G R F T I S K T S T T V D L K I T S P T I E D T A T Y F C A R V D S D S S G A F D R L D L W G Q G T L V T V S S

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 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 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
D P M L T Q T A A S V E V A V G G T V T I K C Q A S Q S I G G Y L S W Y Q Q K P G Q R P K L L I Y R A S T L A S G V P S R F K G S G S G T E Y T L T F S G V E C A D A A A Y Y C Q Q G Y T S S D I N N A F G G G T E V V V K

Antigen Details
Antigen chainsF
Antigen typeprotein
Antigen namemajor capsid protein l1
Antigen speciesHUMAN PAPILLOMAVIRUS TYPE 16
Antigen sequenceMSLWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYRVFRIHLPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGISGHPLLNKLDDTENASAYAANAGVDNRECISMDYKQTQLCLIGCKPPIGEHWGKGSPCTNVAVNPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSICKYPDYIKMVSEPYGDSLFFYLRREQMFVRHLFNRAGAVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMVTSDAQIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNFKEYLRHGEEYDLQFIFQLCKITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVTSQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFSADLDQFPLGRKFLLQAGLKAKPKFTLGKRKATPTTSSTSTTAKRKKRKL

CDR Sequences (chothia definition)
CDRH1GFTMSRY
CDRH2YARNSD
CDRH3VDSDSSGAFDRLDL
CDRL1QASQSIGGYLS
CDRL2RASTLAS
CDRL3QQGYTSSDINNA

Orientation Angles (from ABangle)
HL-50.12°
HC170.57°
HC2119.72°
LC1121.81°
LC286.26°
dc17.0Å
>   M/m
Fv Details
Heavy chainM
Light chainm
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesORYCTOLAGUS CUNICULUS
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 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 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
Q S V K E S E G R L V T P G T P L T L T C T A S G F T M S R Y H M T W V R Q A P G K G L E W I G I I Y A R N S D T Y Y A N W A K G R F T I S K T S T T V D L K I T S P T I E D T A T Y F C A R V D S D S S G A F D R L D L W G Q G T L V T V S S

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 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 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
D P M L T Q T A A S V E V A V G G T V T I K C Q A S Q S I G G Y L S W Y Q Q K P G Q R P K L L I Y R A S T L A S G V P S R F K G S G S G T E Y T L T F S G V E C A D A A A Y Y C Q Q G Y T S S D I N N A F G G G T E V V V K

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen namemajor capsid protein l1
Antigen speciesHUMAN PAPILLOMAVIRUS TYPE 16
Antigen sequenceMSLWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYRVFRIHLPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGISGHPLLNKLDDTENASAYAANAGVDNRECISMDYKQTQLCLIGCKPPIGEHWGKGSPCTNVAVNPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSICKYPDYIKMVSEPYGDSLFFYLRREQMFVRHLFNRAGAVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMVTSDAQIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNFKEYLRHGEEYDLQFIFQLCKITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVTSQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFSADLDQFPLGRKFLLQAGLKAKPKFTLGKRKATPTTSSTSTTAKRKKRKL

CDR Sequences (chothia definition)
CDRH1GFTMSRY
CDRH2YARNSD
CDRH3VDSDSSGAFDRLDL
CDRL1QASQSIGGYLS
CDRL2RASTLAS
CDRL3QQGYTSSDINNA

Orientation Angles (from ABangle)
HL-52.37°
HC170.15°
HC2120.16°
LC1122.27°
LC284.35°
dc17.35Å
>   J/j
Fv Details
Heavy chainJ
Light chainj
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesORYCTOLAGUS CUNICULUS
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 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 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
Q S V K E S E G R L V T P G T P L T L T C T A S G F T M S R Y H M T W V R Q A P G K G L E W I G I I Y A R N S D T Y Y A N W A K G R F T I S K T S T T V D L K I T S P T I E D T A T Y F C A R V D S D S S G A F D R L D L W G Q G T L V T V S S

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 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 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
D P M L T Q T A A S V E V A V G G T V T I K C Q A S Q S I G G Y L S W Y Q Q K P G Q R P K L L I Y R A S T L A S G V P S R F K G S G S G T E Y T L T F S G V E C A D A A A Y Y C Q Q G Y T S S D I N N A F G G G T E V V V K

Antigen Details
Antigen chainsB
Antigen typeprotein
Antigen namemajor capsid protein l1
Antigen speciesHUMAN PAPILLOMAVIRUS TYPE 16
Antigen sequenceMSLWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYRVFRIHLPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGISGHPLLNKLDDTENASAYAANAGVDNRECISMDYKQTQLCLIGCKPPIGEHWGKGSPCTNVAVNPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSICKYPDYIKMVSEPYGDSLFFYLRREQMFVRHLFNRAGAVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMVTSDAQIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNFKEYLRHGEEYDLQFIFQLCKITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVTSQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFSADLDQFPLGRKFLLQAGLKAKPKFTLGKRKATPTTSSTSTTAKRKKRKL

CDR Sequences (chothia definition)
CDRH1GFTMSRY
CDRH2YARNSD
CDRH3VDSDSSGAFDRLDL
CDRL1QASQSIGGYLS
CDRL2RASTLAS
CDRL3QQGYTSSDINNA

Orientation Angles (from ABangle)
HL-52.36°
HC170.39°
HC2118.98°
LC1121.4°
LC284.46°
dc17.06Å
>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesORYCTOLAGUS CUNICULUS
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 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 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
Q S V K E S E G R L V T P G T P L T L T C T A S G F T M S R Y H M T W V R Q A P G K G L E W I G I I Y A R N S D T Y Y A N W A K G R F T I S K T S T T V D L K I T S P T I E D T A T Y F C A R V D S D S S G A F D R L D L W G Q G T L V T V S S

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 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 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
D P M L T Q T A A S V E V A V G G T V T I K C Q A S Q S I G G Y L S W Y Q Q K P G Q R P K L L I Y R A S T L A S G V P S R F K G S G S G T E Y T L T F S G V E C A D A A A Y Y C Q Q G Y T S S D I N N A F G G G T E V V V K

Antigen Details
Antigen chainsD
Antigen typeprotein
Antigen namemajor capsid protein l1
Antigen speciesHUMAN PAPILLOMAVIRUS TYPE 16
Antigen sequenceMSLWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYRVFRIHLPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGISGHPLLNKLDDTENASAYAANAGVDNRECISMDYKQTQLCLIGCKPPIGEHWGKGSPCTNVAVNPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSICKYPDYIKMVSEPYGDSLFFYLRREQMFVRHLFNRAGAVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMVTSDAQIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNFKEYLRHGEEYDLQFIFQLCKITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVTSQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFSADLDQFPLGRKFLLQAGLKAKPKFTLGKRKATPTTSSTSTTAKRKKRKL

CDR Sequences (chothia definition)
CDRH1GFTMSRY
CDRH2YARNSD
CDRH3VDSDSSGAFDRLDL
CDRL1QASQSIGGYLS
CDRL2RASTLAS
CDRL3QQGYTSSDINNA

Orientation Angles (from ABangle)
HL-52.6°
HC170.11°
HC2118.27°
LC1121.59°
LC284.59°
dc16.87Å
>   K/k
Fv Details
Heavy chainK
Light chaink
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesORYCTOLAGUS CUNICULUS
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 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 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
Q S V K E S E G R L V T P G T P L T L T C T A S G F T M S R Y H M T W V R Q A P G K G L E W I G I I Y A R N S D T Y Y A N W A K G R F T I S K T S T T V D L K I T S P T I E D T A T Y F C A R V D S D S S G A F D R L D L W G Q G T L V T V S S

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 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 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
D P M L T Q T A A S V E V A V G G T V T I K C Q A S Q S I G G Y L S W Y Q Q K P G Q R P K L L I Y R A S T L A S G V P S R F K G S G S G T E Y T L T F S G V E C A D A A A Y Y C Q Q G Y T S S D I N N A F G G G T E V V V K

Antigen Details
Antigen chainsC
Antigen typeprotein
Antigen namemajor capsid protein l1
Antigen speciesHUMAN PAPILLOMAVIRUS TYPE 16
Antigen sequenceMSLWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYRVFRIHLPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGISGHPLLNKLDDTENASAYAANAGVDNRECISMDYKQTQLCLIGCKPPIGEHWGKGSPCTNVAVNPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSICKYPDYIKMVSEPYGDSLFFYLRREQMFVRHLFNRAGAVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMVTSDAQIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNFKEYLRHGEEYDLQFIFQLCKITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVTSQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFSADLDQFPLGRKFLLQAGLKAKPKFTLGKRKATPTTSSTSTTAKRKKRKL

CDR Sequences (chothia definition)
CDRH1GFTMSRY
CDRH2YARNSD
CDRH3VDSDSSGAFDRLDL
CDRL1QASQSIGGYLS
CDRL2RASTLAS
CDRL3QQGYTSSDINNA

Orientation Angles (from ABangle)
HL-51.31°
HC170.09°
HC2119.27°
LC1122.1°
LC285.71°
dc17.24Å
>   Downloads

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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