4KXJ,1SSK,2BTL,2BXX,2GEC,2OG3,3HD4,4LI4,4LM9,4UD1,5N4K,7CDZ


Conserved Protein Domain Family
CoV_N-NTD
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cd21554: CoV_N-NTD 
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N-terminal domain of nucleocapsid (N) protein of coronavirus
The coronavirus nucleocapsid (N) protein is a major structural and multifunctional protein. It plays an important role in the virus replication cycle, by forming a complex with the viral RNA through its N-terminal domain (N-NTD), which makes this domain an important drug target. It also interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly.
Links
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Statistics
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PSSM-Id: 439219
Aligned: 108 rows
Threshold Bit Score: 115.761
Created: 13-Oct-2021
Updated: 25-Oct-2021
Structure
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Program:
Drawing:
Aligned Rows:
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RNA binding
Conserved site includes 13 residues -Click on image for an interactive view with Cn3D
Feature 1:RNA binding site [nucleic acid binding site]
Evidence:
  • Comment:based on the binding of human CoV nucleoprotein to ribonucleoside 5'-monophosphates
  • Structure:4LM9: Human coronavirus OC43 nucleoprotein with bound GMP, contacts 4A
    - View structure with Cn3D
  • Structure:4LI4: Human coronavirus OC43 nucleoprotein with bound AMP, contacts 4A
    - View structure with Cn3D
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Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1        ########                                                      # # #             
4KXJ_A         6 PYYSWFSGITQFqk-gKEFEFVegQGVPIAPGVPATEAKGYWYRHNRRSFktadgnqrqLLPRWYFYYLGTGPHAKDQYG 84  Human coronavir...
4LM9_A         6 PYYSWFSGITQFqk-gKEFEFVegQGVPIAPGVPATEAKGYWYRHNRRSFktadgnqrqLLPRWYFYYLGTGPHAKDQYG 84  Human coronavir...
CAI40297      37 GSASWFQALKSRkpdgPEPHFPg-SGVPVNDNVDPKASHGYWRRQRRFKPgkgg--rkpVGDAWYFYYTGTGPLADLQYA 113 Goose coronavirus
ACJ12048       9 TDASWFQVLKAQnkkaTHPKFKg-DGVPINSAIKPAENHGYWLRYNRQKPgg-----tqIPPSYAFYYTGTGPRGNLKYG 82  Bulbul coronavi...
YP_005352867   9 ADASWFQPIKAQnkkiTAPSFKk-NGVPVNASLQAADQHGYWLRYNRTKSgg-----gsIPAAFSFYYTGTGPYATLKFG 82  Night heron cor...
YP_005352875   9 ADCSWFQIIKAQnkkvQPLAFKg-DGVPINTTLPKEMCHGYWLRYKRVKPgg-----apLPPSYSFYYTGTGPRATLKYG 82  Wigeon coronavi...
YP_005352885   9 ADASWFQPLKAQnkknTTPSFKg-DGVPINTSLDHKAAHGYWLRFNRQKPgg-----aqLPPSFAFYYTGTGPRGNLKYG 82  Common moorhen ...
AHB63520      34 GNVSWFQAIKGRkvgeEGITFKg-PGVPVNENVSKNQNHGYWIQRSRTTPgg-----kkLAPLYYFYYTGTGPRDQAKYG 107 Bottlenose dolp...
AKF17732      31 GNASWFQSLKAKklnsPPPTFEg-SGVPDNENLKSSQQHGYWRRQARYKPgkgg--rkpVPDAWYFYYTGTGPFADLKWG 107 Duck coronavirus
BBC54826       9 VDASWFQVLKAQnkkaTHPQFRg-DGVPINSAIKAPENHGYWLRFNRQKPgg-----aaIPPSYAFYYTGTGPRGNLKFG 82  Falcon coronavi...

Feature 1                                        #        #                 
4KXJ_A        85 TDI--------DGVYWVASNQADVntPADIVDRDpss--deAIPTRFPpgtVLPQGYYI 133 Human coronavirus OC43
4LM9_A        85 TDI--------DGVYWVASNQADVntPADIVDRDpss--deAIPTRFPpgtVLPQGYYI 133 Human coronavirus OC43
CAI40297     114 DPH--------EDVVWVKAKGADTstRSKQGTRDpdk--fdQFPLRFAd-gGPDNGFRW 161 Goose coronavirus
ACJ12048      83 EYPpndn-ietSRITWVKAKGADTsvKPKVAKRNpsnpkhnLLPLRFPagdGPAQGFRV 140 Bulbul coronavirus HKU11-796
YP_005352867  83 ETPs-------DRITWVKGPSAVTtnKPKVAKRDpdk--hpLLPLTFPpgdGVNTGLRV 132 Night heron coronavirus HKU19
YP_005352875  83 ELQdsdnqdnvNRVLWVKSPDADTsiKPKVAKRNpdk--hpLLPLRFKpgdGPVQGFRI 139 Wigeon coronavirus HKU20
YP_005352885  83 EFPpnes-kgnSRITWVHVKDADTsiKPKVAKRNpqnpkhaLLPLRFPpgdGPAQGFRI 140 Common moorhen coronavirus HKU21
AHB63520     108 QDI--------PYVTWVKGEGAKTsqLSEAGSRDvnk-fpnAFPLIFPtgdGPDRGFFI 157 Bottlenose dolphin coronavirus HKU22
AKF17732     108 QPH--------DDIVWVAVDGADVdvKSGQGTRDpdk--fdQFPLRFAe-gGPDDNFRW 155 Duck coronavirus
BBC54826      83 EFPpnds-kenSRITWVKAKGANTdlKPHVAKRNpnnpkhaLLPLRFPtgdGPAPGFRV 140 Falcon coronavirus UAE-HKU27

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