5GMQ - JenaLib

Title :   STRUCTURE OF MERS-COV RBD IN COMPLEX WITH A FULLY HUMAN ANTIBODY MCA1

Authors :   C. Chen, J. M. Wang, T. T. Zou, X. P. Gao, S. Cui, Q. Jin

Date :   15 Jul 16 (Deposition) - 31 May 17 (Release) - 31 May 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Chen, L. Bao, C. Chen, T. Zou, Y. Xue, F. Li, Q. Lv, S. Gu, X. Gao, S. Cui, J. Wang, C. Qin, Q. Jin
Human Neutralizing Monoclonal Antibody Efficiently Inhibits Mers-Cov Replication In Common Marmoset.
J. Infect. Dis. 2017
PubMed-ID: 28472421 | Reference-DOI: 10.1093/INFDIS/JIX209

Compounds

Molecule 1 - S PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	INSECT CELL EXPRESSION VECTOR PTIE1
	Expression System Taxid	:	266783
	Fragment	:	UNP RESIDUES 367-588
	Organism Scientific	:	MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS
	Organism Taxid	:	1335626

Molecule 2 - MCA1 HEAVY CHAIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	MAMMALIAN EXPRESSION VECTOR PCBIO
	Expression System Taxid	:	386595
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - MCA1 LIGHT CHAIN
	Chains	:	C
	Engineered	:	YES
	Expression System	:	MAMMALIAN EXPRESSION VECTOR PCBIO
	Expression System Taxid	:	386595
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Structural Features

Chains, Units

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 4)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE B:108 , ASP B:109 , ARG C:44 , LEU C:45 , ILE C:57	binding site for residue EDO C 301
2	AC2	SOFTWARE	SER A:416 , SER A:419 , VAL A:420 , ASN A:421 , HOH A:704 , ALA B:-2 , ARG B:0	binding site for Poly-Saccharide residues NAG A 601 through MAN A 603

SS Bonds (8, 8)

Asymmetric/Biological Unit

No.	Residues
1	A:383	-	A:407
2	A:425	-	A:478
3	A:437	-	A:585
4	A:503	-	A:526
5	B:19	-	B:93
6	B:148	-	B:204
7	C:21	-	C:87
8	C:133	-	C:193

Cis Peptide Bonds (8, 8)

Asymmetric/Biological Unit

No.	Residues
1	Gly B:63	-	Arg B:64
2	Phe B:154	-	Pro B:155
3	Glu B:156	-	Pro B:157
4	Ser C:5	-	Pro C:6
5	Gly C:49	-	Ala C:50
6	Ser C:93	-	Pro C:94
7	Tyr C:139	-	Pro C:140
8	Val C:149	-	Asp C:150

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:205
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh....hhhhheeeee.....hhhhhhh..eeeeeeee..hhhhhh.....eeeeeeee.hhhhhhhhh....hhhhhh.........eeeeeee.............eeeeeeeeee......eee........hhhhhh..........eeeee........eeeeeeeee......eeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gmq A 381 VECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRLLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTNSVCPK 587
                                   390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       582     
                                                                                                                                                                                                                               578|      
                                                                                                                                                                                                                                581

Chain B from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeeehhhhh..ee.......eeeeee....eeeeee........eeeeeee.......hhhhh..ee....eeee.........eeee......ee..eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhhhhh.eeeeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gmq B  -2 ATRLEESGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGRIIPILGIANYAQKFQGRVTITADKSTSTAYMELSSLRSEDTAVYYCASKQGDYYDRTSYAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 222
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217

Chain C from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee....hhh.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeee.....................eeeeeeeeeehhhhh....eeeee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gmq C  -1 DVELTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDLQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKYACEVTHQGLSSPVTKSFNR 210
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148 ||    160       170       180       191       201         
                                                                                                                                                                                 150|                                 189|                   
                                                                                                                                                                                  153                                  191

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MAN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu B:156 - Pro B:157	[ RasMol ]
		Gly B:63 - Arg B:64	[ RasMol ]
		Gly C:49 - Ala C:50	[ RasMol ]
		Phe B:154 - Pro B:155	[ RasMol ]
		Ser C:5 - Pro C:6	[ RasMol ]
		Ser C:93 - Pro C:94	[ RasMol ]
		Tyr C:139 - Pro C:140	[ RasMol ]
		Val C:149 - Asp C:150	[ RasMol ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	5gmq
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	V5RDT9_9BETC \| V5RDT9
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	V5RDT9_9BETC \| V5RDT9
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (2, 2)

SS Bonds (8, 8)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File