4QHL - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   I3.2 (UNBOUND) FROM CH103 LINEAGE

Authors :   D. Fera, S. C. Harrison

Date :   28 May 14 (Deposition) - 11 Jun 14 (Release) - 30 Jul 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.15

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Fab Fragment, Hiv-1, Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Fera, A. G. Schmidt, B. F. Haynes, F. Gao, H. X. Liao, T. B. Kepler, S. C. Harrison
Affinity Maturation In An Hiv Broadly Neutralizing B-Cell Lineage Through Reorientation Of Variable Domains.
Proc. Natl. Acad. Sci. Usa V. 111 10275 2014
PubMed-ID: 24982157 | Reference-DOI: 10.1073/PNAS.1409954111

Molecule 1 - I3 HEAVY CHAIN
	Cell Line	:	HEK 293T
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK 293T
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PVRC-8400
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Fragment	:	FAB
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - UCA LIGHT CHAIN
	Cell Line	:	HEK 293T
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK 293T
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PVRC-8400
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Fragment	:	FAB
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4QHL)

(no "Site" information available for 4QHL)

Asymmetric Unit

No.	Residues
1	A:22	-	A:92
2	A:140	-	A:196
3	B:23	-	B:88
4	B:134	-	B:193
5	C:22	-	C:92
6	C:140	-	C:196
7	D:23	-	D:88
8	D:134	-	D:193

Asymmetric Unit

No.	Residues
1	Ser A:132	-	Gly A:133
2	Phe A:146	-	Pro A:147
3	Glu A:148	-	Pro A:149
4	Asp B:26	-	Lys B:27
5	Lys B:27	-	Leu B:28
6	Tyr B:140	-	Pro B:141
7	Phe C:146	-	Pro C:147
8	Glu C:148	-	Pro C:149
9	Asp D:26	-	Lys D:27
10	Gly D:29	-	Asp D:30
11	Tyr D:140	-	Pro D:141

(no "SAP(SNP)/Variant" information available for 4QHL)

(no "PROSITE Motif" information available for 4QHL)

(no "Exon" information available for 4QHL)

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:223
                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeee....eeeeeeee......eeeeeeeee...eeeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeee.........eee...eeeeee.......eeeee...........eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhh....eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4qhl A    1 QVQLQESGPGLVKSSETLSLTCTVSGGSMGGYYWSWLRQSPVKGLEWIGYIFHTGHTNYNPSLESRVTVSVDTSENQFSLRLRSVTAADTAVYYCASLPRGQLVNAFFDNWGQGTLVTVASASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  215
                                    10        20        30        40        50        60        70        80  |||   87        97   ||||102       112       122       132       142       152       162       172       182       192       202       212   
                                                                                                            82A||               100A||||                                                                                                                   
                                                                                                             82B|                100B|||                                                                                                                   
                                                                                                              82C                 100C||                                                                                                                   
                                                                                                                                   100D|                                                                                                                   
                                                                                                                                    100E

Chain B from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee......eeeeee.........eeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee.......ee...eeee.........eeeee..hhhhhh...eeeeeeeeee....eeeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4qhl B    2 YELTQPPSVSVSPGQTASITCSGDKLGDKYACWYQQKPGQSPVLVIYQDSKRPSGIPERFSGSNSGNTATLTISGTQAMDEADYYCQAWDSFSTFVFGTGTKVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  209
                                   |12        22        32        42        52        62        72        82        92   |   101     | 110       120       130       140       150       160       170       180       190       200         
                                   9|                                                                                  95A        106A                                                                                                       
                                   11

Chain C from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee......eeeeeeeee...eeeeeeee.....eee.......eeeeeehhh.eeeeee........eeeeeeeee.........eee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4qhl C    1 QVQLQESGPGLVKSSETLSLTCTVSGGSMGGYYWSWLRQSPVKGLEWIGYIFHTGHTNYNPSLESRVTVSVDTSENQFSLRLRSVTAADTAVYYCASLPRGQLVNAFFDNWGQGTLVTVASASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  215
                                    10        20        30        40        50        60        70        80  |||   87        97   ||||102       112       122     ||136       146       156       166       176       186       196       206         
                                                                                                            82A||               100A||||                         128|                                                                                  
                                                                                                             82B|                100B|||                          133                                                                                  
                                                                                                              82C                 100C||                                                                                                               
                                                                                                                                   100D|                                                                                                               
                                                                                                                                    100E

Chain D from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee......eeeee..........eeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee.......ee...eeee.........eeeee..hhhhhh...eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4qhl D    2 YELTQPPSVSVSPGQTASITCSGDKLGDKYACWYQQKPGQSPVLVIYQDSKRPSGIPERFSGSNSGNTATLTISGTQAMDEADYYCQAWDSFSTFVFGTGTKVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  209
                                   |12        22        32        42        52        62        72        82        92   |   101     | 110       120       130       140       150       160       170       180       190       200         
                                   9|                                                                                  95A        106A                                                                                                       
                                   11

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 '\|'

(no "SCOP Domain" information available for 4QHL)

(no "CATH Domain" information available for 4QHL)

(no "Pfam Domain" information available for 4QHL)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4QHL)

Asymmetric 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
(no "Ligands, Modified Residues, Ions" information available for 4qhl)

	Sites
(no "Sites" information available for 4qhl)

	Cis Peptide Bonds
		Asp B:26 - Lys B:27	[ RasMol ]
		Asp D:26 - Lys D:27	[ RasMol ]
		Glu A:148 - Pro A:149	[ RasMol ]
		Glu C:148 - Pro C:149	[ RasMol ]
		Gly D:29 - Asp D:30	[ RasMol ]
		Lys B:27 - Leu B:28	[ RasMol ]
		Phe A:146 - Pro A:147	[ RasMol ]
		Phe C:146 - Pro C:147	[ RasMol ]
		Ser A:132 - Gly A:133	[ RasMol ]
		Tyr B:140 - Pro B:141	[ RasMol ]
		Tyr D:140 - Pro D:141	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 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)

Access by PDB/NDB ID
	4qhl
		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
	Q6GMX6_HUMAN \| Q6GMX6
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

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

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
	Q6GMX6_HUMAN \| Q6GMX6
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (11, 11)

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 (0, 0)

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