4JDV - 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 GERM-LINE PRECURSOR OF NIH45-46 FAB

Authors :   R. Diskin, L. Scharf, P. J. Bjorkman

Date :   25 Feb 13 (Deposition) - 20 Mar 13 (Release) - 08 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Ig Fold, Anti Hiv Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Scharf, A. P. West, H. Gao, T. Lee, J. F. Scheid, M. C. Nussenzweig, P. J. Bjorkman, R. Diskin
Structural Basis For Hiv-1 Gp120 Recognition By A Germ-Line Version Of A Broadly Neutralizing Antibody.
Proc. Natl. Acad. Sci. Usa V. 110 6049 2013
PubMed-ID: 23524883 | Reference-DOI: 10.1073/PNAS.1303682110

Molecule 1 - FAB HEAVY CHAIN
	Chains	:	A, H
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Strain	:	HEK293-6E
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Fragment	:	NIH45-46 GERM-LINE HEAVY CHAIN, IG GAMMA-1 CHAIN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - FAB LIGHT CHAIN
	Chains	:	B, L
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Strain	:	HEK293-6E
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Fragment	:	NIH45-46 GERM-LINE LIGHT CHAIN, IG KAPPA
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	144	2	Ligand/Ion	TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2	1PE	2	Ligand/Ion	PENTAETHYLENE GLYCOL
3	GOL	2	Ligand/Ion	GLYCEROL
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	144	1	Ligand/Ion	TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2	1PE	-1	Ligand/Ion	PENTAETHYLENE GLYCOL
3	GOL	2	Ligand/Ion	GLYCEROL
4	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	144	1	Ligand/Ion	TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2	1PE	2	Ligand/Ion	PENTAETHYLENE GLYCOL
3	GOL	-1	Ligand/Ion	GLYCEROL
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:82B , ARG A:83 , HOH A:475 , HOH A:552 , HOH A:614 , HOH A:661 , SER H:54 , GLY H:56 , HOH H:463	BINDING SITE FOR RESIDUE SO4 A 301
02	AC2	SOFTWARE	SER A:7 , GLY A:8 , HOH A:500 , HOH A:637 , ARG L:18 , THR L:20 , HOH L:455 , HOH L:505	BINDING SITE FOR RESIDUE SO4 A 302
03	AC3	SOFTWARE	PHE A:170 , PRO A:171 , SER A:181 , LEU A:182 , SER A:183 , HOH A:477 , SER B:172 , SER B:173 , THR B:174	BINDING SITE FOR RESIDUE GOL A 303
04	AC4	SOFTWARE	GLU A:152 , PRO A:153 , VAL A:154 , PHE A:170 , ALA A:172 , LEU A:182 , HOH A:615	BINDING SITE FOR RESIDUE 144 A 304
05	AC5	SOFTWARE	LYS B:186 , ARG B:207 , HOH B:617 , HOH B:635	BINDING SITE FOR RESIDUE SO4 B 301
06	AC6	SOFTWARE	HIS A:168 , HOH A:519 , GLU B:161 , GLN B:162 , ASP B:163 , HOH B:425 , HOH B:464	BINDING SITE FOR RESIDUE GOL B 302
07	AC7	SOFTWARE	GLU H:152 , PRO H:153 , VAL H:154 , PHE H:170 , ALA H:172 , LEU H:182	BINDING SITE FOR RESIDUE 144 H 301
08	AC8	SOFTWARE	GLN A:61 , TRP H:50 , ASN H:58 , TRP H:102 , HOH H:449 , HOH H:458 , HOH H:515 , HOH H:573 , TYR L:91 , GLU L:92 , HOH L:549	BINDING SITE FOR RESIDUE 1PE H 302
09	AC9	SOFTWARE	LYS H:62 , GLN H:64 , LYS L:186 , ARG L:207	BINDING SITE FOR RESIDUE SO4 L 301
10	BC1	SOFTWARE	GLY A:138 , THR A:139 , VAL A:188 , PRO A:189 , HOH A:612 , HOH A:642 , GLN L:37 , LYS L:39 , ARG L:45 , PRO L:59 , ALA L:60 , ARG L:61 , GLU L:81 , HOH L:418	BINDING SITE FOR RESIDUE 1PE L 302

Asymmetric Unit

No.	Residues
1	A:22	-	A:92
2	A:144	-	A:200
3	B:23	-	B:88
4	B:130	-	B:190
5	H:22	-	H:92
6	H:144	-	H:200
7	L:23	-	L:88
8	L:130	-	L:190

Asymmetric Unit

No.	Residues
1	Phe A:150	-	Pro A:151
2	Glu A:152	-	Pro A:153
3	Ser B:7	-	Pro B:8
4	Tyr B:136	-	Pro B:137
5	Phe H:150	-	Pro H:151
6	Glu H:152	-	Pro H:153
7	Ser L:7	-	Pro L:8
8	Tyr L:136	-	Pro L:137

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

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

(no "Exon" information available for 4JDV)

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:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee..hhhhh.....eeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee...hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jdv A   2 VQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARGKYCTARDYYNWDFQHWGQGTLVTVSSASTKGPSVFPLAPSSKGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH 224
                                    11        21        31        41        51 |      60        70        80  |||   87        97  |||| 103       113       123       133|      147       157       167       177       187       197       207       217       
                                                                             52A                            82A||               99A|||                               133|                                                                                      
                                                                                                             82B|                99B||                                138                                                                                      
                                                                                                              82C                 99C|                                                                                                                         
                                                                                                                                   99D

Chain B from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains d4jdvb1 B:2-103 automated matches                                                                     d4jdvb2 B:104-209 automated matches                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeee........eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee..ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jdv B   2 IVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQYEFFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 209
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201

Chain H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee..hhhhh.....eeee...eeeee........eeeeeeee.eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhh...eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jdv H   2 VQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARGKYCTARDYYNWDFQHWGQGTLVTVSSASTKGPSVFPLAPSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLQTYICNVNHKPSNTKVDKRVEP 217
                                    11        21        31        41        51 |      60        70        80  |||   87        97  |||| 103       113       123       140       150       160       170       180       190  ||   202       212     
                                                                             52A                            82A||               99A|||                             131|                                                   193|                     
                                                                                                             82B|                99B||                              139                                                    196                     
                                                                                                              82C                 99C|                                                                                                             
                                                                                                                                   99D

Chain L from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains d4jdvl1 L:1-103 automated matches                                                                      d4jdvl2 L:104-209 automated matches                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeee.....eeeeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee..ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jdv L   1 EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQYEFFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

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: C1 set domains (antibody constant domain-like) (3013)

Protein domain: automated matches (652)

Human (Homo sapiens) [TaxId: 9606] (334)

1a	d4jdvb2	B:104-209
1b	d4jdvl2	L:104-209

Family: V set domains (antibody variable domain-like) (1919)

Protein domain: automated matches (311)

Human (Homo sapiens) [TaxId: 9606] (85)

2a	d4jdvb1	B:2-103
2b	d4jdvl1	L:1-103

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

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

Asymmetric Unit(hide GO term definitions)

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

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
		144	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		1PE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu A:152 - Pro A:153	[ RasMol ]
		Glu H:152 - Pro H:153	[ RasMol ]
		Phe A:150 - Pro A:151	[ RasMol ]
		Phe H:150 - Pro H:151	[ RasMol ]
		Ser B:7 - Pro B:8	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Tyr B:136 - Pro B:137	[ RasMol ]
		Tyr L:136 - Pro L:137	[ 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
	4jdv
		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
	(no 'UniProt ID/Accession number' available) \|
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProt

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
	(no 'UniProt ID/Accession number' available) \|
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT

(no "Entries Sharing at Least One Protein Chain" available for 4JDV)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

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 (2, 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