4NPY - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF GERMLINE FAB PGT121, A PUTATIVE PRECURSOR OF THE BROADLY REACTIVE AND POTENT HIV-1 NEUTRALIZING ANTIBODY

Authors :   J. -P. Julien, D. C. Diwanji, I. A. Wilson

Date :   22 Nov 13 (Deposition) - 11 Dec 13 (Release) - 11 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B,H,L
Biol. Unit 1: H,L  (1x)
Biol. Unit 2: A,B  (1x)

Keywords :   Igg-Fold, Anti-Hiv Antibody Precursor, Hiv Env Gp120, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Sok, U. Laserson, J. Laserson, Y. Liu, F. Vigneault, J. P. Julien, B. Briney, A. Ramos, K. F. Saye, K. Le, A. Mahan, S. Wang, M. Kardar, G. Yaari, L. M. Walker, B. B. Simen, E. P. St John, P. Y. Chan-Hui, K. Swiderek, S. H. Kleinstein, G. Alter, M. S. Seaman, A. K. Chakraborty, D. Koller, I. A. Wilson, G. M. Church, D. R. Burton, P. Poignard
The Effects Of Somatic Hypermutation On Neutralization And Binding In The Pgt121 Family Of Broadly Neutralizing Hiv Antibodies.
Plos Pathog. V. 9 03754 2013
PubMed-ID: 24278016 | Reference-DOI: 10.1371/JOURNAL.PPAT.1003754

Molecule 1 - GERMLINE PGT121 LIGHT CHAIN
	Chains	:	L, A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Fragment	:	FAB
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - GERMLINE PGT121 HEAVY CHAIN
	Chains	:	H, B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Fragment	:	FAB
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric Unit	:	A	B	H	L
Biological Unit 1 (1x)	:			H	L
Biological Unit 2 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	PCA	2	Mod. Amino Acid	PYROGLUTAMIC ACID

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS B:206 , LYS L:149 , ASP L:151 , SER L:152 , SER L:192 , GLU L:203	BINDING SITE FOR RESIDUE GOL L 301
2	AC2	SOFTWARE	SER H:120 , VAL H:121 , VAL H:207 , LYS H:209 , GLU L:123	BINDING SITE FOR RESIDUE GOL H 301
3	AC3	SOFTWARE	TYR A:49 , PRO A:55 , SER A:56 , TYR B:100O , ASP B:101 , HOH B:460 , HOH B:553	BINDING SITE FOR RESIDUE GOL B 301

Asymmetric Unit

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

Asymmetric Unit

No.	Residues
1	Gly L:24	-	Gly L:25
2	Gly L:95	-	Pro L:95A
3	Tyr L:140	-	Pro L:141
4	Phe H:146	-	Pro H:147
5	Glu H:148	-	Pro H:149
6	Gly A:95	-	Pro A:95A
7	Tyr A:140	-	Pro A:141
8	Phe B:146	-	Pro B:147
9	Glu B:148	-	Pro B:149

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

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

(no "Exon" information available for 4NPY)

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:211
                                                                                                                                                                                                                                                    
               SCOP domains d4npya1 A:1-106A automated matches                                                                           d4npya2 A:107-208 automated matches                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeee.......eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4npy A    1 SYVLTQPPSVSVAPGQTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSRGPTNWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAP  208
                                    11        21        31        41        51        61        71        81        91    ||| 98       107       117       127       137       147       157       167       177       187       197       207 
                                    9|                                                                                  95A||        106A                                                                                                      
                                    11                                                                                   95B|                                                                                                                  
                                                                                                                          95C

Chain B from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee......eeeeeee....eee...hhh.eeeeeehhh.eeeeee...hhhhheeeeeeeeeeeeee.....eeeeeeeeee...eeeee........eeeee..hhhhh...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4npy B    1 xVQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPPGKGLEWIGYIYYSGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARTLHGRRIYGIVEWFTYYYMDVWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP  213
                            |       10        20        30        40        50        60        70        80  |||   87        97   |||100J|||||| 104       114       124       134       144       154       164       174       184       194       204         
                            1-PCA                                                                           82A||               100A|||||100M|||                                                                                                                 
                                                                                                             82B|                100B|||||100N||                                                                                                                 
                                                                                                              82C                 100C|||||100O|                                                                                                                 
                                                                                                                                   100D|||||100P                                                                                                                 
                                                                                                                                    100E||||                                                                                                                     
                                                                                                                                     100I|||                                                                                                                     
                                                                                                                                      100J||                                                                                                                     
                                                                                                                                       100K|                                                                                                                     
                                                                                                                                        100L

Chain H from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee......eeeeeee....eee...hhh.eeeeeehhh.eeeeee...hhhhheeeeeeeeeeeeee..hhhhh.eeeeeeeeee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4npy H    1 xVQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPPGKGLEWIGYIYYSGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARTLHGRRIYGIVAFKEWFTYYYMDVWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP  213
                            |       10        20        30        40        50        60        70        80  |||   87        97   |||100G|||||||101       111       121       131       141       151       161       171       181       191       201       211  
                            1-PCA                                                                           82A||               100A|||||100J||||||                                                                                                                 
                                                                                                             82B|                100B|||||100K|||||                                                                                                                 
                                                                                                              82C                 100C|||||100L||||                                                                                                                 
                                                                                                                                   100D|||||100M|||                                                                                                                 
                                                                                                                                    100E|||| 100N||                                                                                                                 
                                                                                                                                     100F|||  100O|                                                                                                                 
                                                                                                                                      100G||   100P                                                                                                                 
                                                                                                                                       100H|                                                                                                                        
                                                                                                                                        100I

Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains d4npyl1 L:1-106A automated matches                                                                           d4npyl2 L:107-209 automated matches                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeee...hhhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeee.......eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4npy L    1 SYVLTQPPSVSVAPGQTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSRGPTNWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPT  209
                                    11        21        31        41        51        61        71        81        91    ||| 98       107       117       127       137       147       157       167       177       187       197       207  
                                    9|                                                                                  95A||        106A                                                                                                       
                                    11                                                                                   95B|                                                                                                                   
                                                                                                                          95C

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Human (Homo sapiens) [TaxId: 9606] (448)

1a	d4npya1	A:1-106A
1b	d4npya2	A:107-208
1c	d4npyl1	L:1-106A
1d	d4npyl2	L:107-209

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

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

Asymmetric Unit(hide GO term definitions)

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

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
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PCA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu B:148 - Pro B:149	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		Gly A:95 - Pro A:95A	[ RasMol ]
		Gly L:24 - Gly L:25	[ RasMol ]
		Gly L:95 - Pro L:95A	[ RasMol ]
		Phe B:146 - Pro B:147	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr L:140 - Pro L: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 \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites 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
	4npy
		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 (2, 5)

Sites (3, 3)

SS Bonds (8, 8)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

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