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(-) Description

Title :  COMPLEX STRUCTURE OF MERS-RBD BOUND WITH 4C2 ANTIBODY
 
Authors :  Y. Li, Y. Wan, P. Liu, J. Zhao, G. Lu, J. Qi, Q. Wang, X. Lu, Y. Wu, W. Liu, K. Y S. Perlman, G. F. Gao, J. Yan
Date :  10 Sep 15  (Deposition) - 14 Oct 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym. Unit :  A,B,C,D,H,L
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,H,L  (1x)
Keywords :  Receptor-Binding Domain Of Mers-Cov Spike, 4C2 Antibody, Neuralization, Receptor-Binding Blocking. , Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Li, Y. Wan, P. Liu, J. Zhao, G. Lu, J. Qi, Q. Wang, X. Lu, Y. Wu, W. Liu, B. Zhang, K. Y. Yuen, S. Perlman, G. F. Gao, J. Yan
A Humanized Neutralizing Antibody Against Mers-Cov Targetin The Receptor-Binding Domain Of The Spike Protein.
Cell Res. V. 25 1237 2015
PubMed-ID: 26391698  |  Reference-DOI: 10.1038/CR.2015.113

(-) Compounds

Molecule 1 - S PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Strain: BL21-GOLD(DE3)PLYSS AG
    Expression System Taxid: 866768
    Fragment: UNP RESIDUES 367-606
    Organism Scientific: MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS
    Organism Taxid: 1335626
 
Molecule 2 - 4C2 HEAVY CHAIN
    Chains: H, C
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - 4C2 LIGHT CHAIN
    Chains: L, D
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDHL
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:487binding site for Mono-Saccharide NAG A 701 bound to ASN A 487

(-) SS Bonds  (18, 18)

Asymmetric Unit
No.Residues
1A:383 -A:407
2A:425 -A:478
3A:437 -A:585
4A:503 -A:526
5B:383 -B:407
6B:425 -B:478
7B:437 -B:585
8B:503 -B:526
9C:22 -C:96
10C:143 -C:198
11C:218 -D:214
12D:23 -D:88
13D:134 -D:194
14H:22 -H:96
15H:143 -H:198
16H:218 -L:214
17L:23 -L:88
18L:134 -L:194

(-) Cis Peptide Bonds  (13, 13)

Asymmetric Unit
No.Residues
1Asp A:580 -Thr A:581
2Phe H:149 -Pro H:150
3Glu H:151 -Pro H:152
4Trp H:191 -Pro H:192
5Leu L:94 -Pro L:95
6Tyr L:140 -Pro L:141
7Asp B:580 -Thr B:581
8Gly C:54 -Gly C:55
9Phe C:149 -Pro C:150
10Glu C:151 -Pro C:152
11Trp C:191 -Pro C:192
12Leu D:94 -Pro D:95
13Tyr D:140 -Pro D:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DO2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DO2)

(-) Exons   (0, 0)

(no "Exon" information available for 5DO2)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh....hhhhheeeee..eeehhhhhhhh.eeeeeeee..hhhhhh.....eeeeeeee.hhhhhhhhh....hhhhhhh........eeeeeee............eeeeeeeeeee......eee........hhhhhh.........eeeeee........eeeeeeeeee.....eeeeeeeee.......eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5do2 A 381 VECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRLLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKL 588
                                   390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580        


Chain B from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh....hhhhheeeee...eehhhhhhhhheeeeeeee..hhhhhh.....eeeeeeee.hhhhhhhhh....hhhhhhh........eeeeeee.............eeeeeeeeee......eee........hhhhhh.........eeeeee........eeeeeeeee......eeeeeeeee........ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5do2 B 381 VECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRLLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKL 588
                                   390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580        


Chain C from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......ee.........eeeee....eeeeee...hhhhheeeeeeee.....ee...eeeee........eeeee......eeeeeeeeeee.....eeee........eee...eee..eeeeeeeeeee.hhhhhh..eeeeee....eeeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5do2 C   1 DVKLVESGGGLVKPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVATISSGGSYTYYPDSVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCTRDGNDYDYWGQGTTLTVSSAKTTPPSVYPLAPGSNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCG 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130||     144       154       164       174       184       194       204       214     
                                                                                                                                                            131|                                                                                   
                                                                                                                                                             136                                                                                   


Chain D from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5do2 D   1 DIQMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    


Chain H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeeee.....ee...eeeee........eeeee......eeeeeeeeeee.....eeee........eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5do2 H   1 DVKLVESGGGLVKPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVATISSGGSYTYYPDSVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCTRDGNDYDYWGQGTTLTVSSAKTTPPSVYPLAPGSNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCG 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130||     144       154       164       174       184       194       204       214     
                                                                                                                                                            131|                                                                                   
                                                                                                                                                             136                                                                                   


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5do2 L   1 DIQMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5DO2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DO2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DO2)

(-) Gene Ontology  (5, 10)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        K0BRG7_9BETC | K0BRG7: 4kqz 4kr0 4mod

(-) Related Entries Specified in the PDB File

4kr0 THE COMPLEX STRUCTURE BETWEEN MERS-RBD AND ITS RECEPTOR CD26.