2NY7 - JenaLib

Asym.Unit - manually (Jmol Viewer)

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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   HIV-1 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH THE BROADLY NEUTRALIZING CD4-BINDING-SITE ANTIBODY B12

Authors :   T. Zhou, L. Xu, B. Dey, A. J. Hessell, D. Van Ryk, S. H. Xiang, X. Yang, M. Y M. B. Zwick, J. Arthos, D. R. Burton, D. S. Dimitrov, J. Sodroski, R. Wya G. J. Nabel, P. D. Kwong

Date :   20 Nov 06 (Deposition) - 06 Feb 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : G,H,L
Biol. Unit 1: G,H,L  (1x)
Biol. Unit 2: G,H,L  (2x)
Biol. Unit 3: G (2x),H (2x),L (2x)
Biol. Unit 4: G (2x),H (2x),L (2x)
Biol. Unit 5: G,H,L  (2x)

Keywords :   Hiv, Gp120, Broadly Neutralizing Antibody, B12, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Zhou, L. Xu, B. Dey, A. J. Hessell, D. Van Ryk, S. H. Xiang, X. Yang, M. Y. Zhang, M. B. Zwick, J. Arthos, D. R. Burton, D. S. Dimitrov, J. Sodroski, R. Wyatt, G. J. Nabel, P. D. Kwong
Structural Definition Of A Conserved Neutralization Epitope On Hiv-1 Gp120.
Nature V. 445 732 2007
PubMed-ID: 17301785 | Reference-DOI: 10.1038/NATURE05580

Molecule 1 - ENVELOPE GLYCOPROTEIN GP120
	Chains	:	G
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	EMBRYONIC CELL LINE 293
	Expression System Common	:	HUMAN
	Expression System Organ	:	KIDNEY
	Expression System Plasmid	:	CMVR
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Fragment	:	CORE
	Mutation	:	YES
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676
	Strain	:	HXBC2

Molecule 2 - ANTIBODY B12, HEAVY CHAIN
	Chains	:	H
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Plasmid	:	PDR12
	Expression System Strain	:	CHO-K1
	Expression System Taxid	:	10029
	Expression System Vector Type	:	PLASMID
	Fragment	:	ANTIGEN-BINDING FRAGMENT, FAB
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - ANTIBODY B12, LIGHT CHAIN
	Chains	:	L
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Plasmid	:	PDR12
	Expression System Strain	:	CHO-K1
	Expression System Taxid	:	10029
	Expression System Vector Type	:	PLASMID
	Fragment	:	ANTIGEN-BINDING FRAGMENT, FAB
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3
Asymmetric Unit	:	G	H	L
Biological Unit 1 (1x)	:	G	H	L
Biological Unit 2 (2x)	:	G	H	L
Biological Unit 3 (2x)	:	G (2x)	H (2x)	L (2x)
Biological Unit 4 (2x)	:	G (2x)	H (2x)	L (2x)
Biological Unit 5 (2x)	:	G	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 13)

No.	Name	Count	Type	Full Name
1	NAG	13	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 13)

No.	Name	Count	Type	Full Name
1	NAG	13	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (1, 26)

No.	Name	Count	Type	Full Name
1	NAG	26	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 3 (1, 26)

No.	Name	Count	Type	Full Name
1	NAG	26	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 4 (1, 26)

No.	Name	Count	Type	Full Name
1	NAG	26	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 5 (1, 26)

No.	Name	Count	Type	Full Name
1	NAG	26	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN G:234 , THR G:236 , GLY G:237 , HOH G:1025	BINDING SITE FOR RESIDUE NAG G 734
02	AC2	SOFTWARE	VAL G:85 , ASN G:229 , ASN G:241	BINDING SITE FOR RESIDUE NAG G 741
03	AC3	SOFTWARE	ARG G:252 , ASN G:262 , PHE G:376 , ASN G:377 , CYS G:378 , SER G:446 , SER G:447 , HOH G:998	BINDING SITE FOR RESIDUE NAG G 762
04	AC4	SOFTWARE	ASN G:276 , ASP G:279 , HOH G:1030	BINDING SITE FOR RESIDUE NAG G 776
05	AC5	SOFTWARE	GLU G:268 , GLU G:269 , VAL G:270 , ASN G:289 , THR G:290 , GLN G:344	BINDING SITE FOR RESIDUE NAG G 789
06	AC6	SOFTWARE	ASN G:295 , ALA G:334	BINDING SITE FOR RESIDUE NAG G 795
07	AC7	SOFTWARE	ARG G:335 , ASN G:339 , TRP G:400	BINDING SITE FOR RESIDUE NAG G 839
08	AC8	SOFTWARE	PHE G:353 , GLY G:354 , ASN G:356 , LYS G:357 , ASN G:463 , HOH G:992	BINDING SITE FOR RESIDUE NAG G 856
09	AC9	SOFTWARE	ASN G:386 , THR G:388 , HOH G:975 , HOH G:989 , TRP H:100 , HOH H:300	BINDING SITE FOR RESIDUE NAG G 886
10	BC1	SOFTWARE	ASN G:392	BINDING SITE FOR RESIDUE NAG G 892
11	BC2	SOFTWARE	ILE G:360 , THR G:394 , ASN G:397 , SER G:398 , HOH G:1050 , GLY H:15	BINDING SITE FOR RESIDUE NAG G 897
12	BC3	SOFTWARE	ASN G:262 , SER G:291 , ASN G:448 , HOH G:1033	BINDING SITE FOR RESIDUE NAG G 948
13	BC4	SOFTWARE	ASN G:463 , HOH G:991 , LYS H:13	BINDING SITE FOR RESIDUE NAG G 963

Asymmetric Unit

No.	Residues
1	G:96	-	G:275
2	G:109	-	G:428
3	G:119	-	G:205
4	G:218	-	G:247
5	G:228	-	G:239
6	G:296	-	G:331
7	G:378	-	G:445
8	G:385	-	G:418
9	H:22	-	H:92
10	H:142	-	H:208
11	H:230	-	L:214
12	L:23	-	L:88
13	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Arg G:252	-	Pro G:253
2	Phe H:148	-	Pro H:149
3	Glu H:150	-	Pro H:151
4	Ser L:7	-	Pro L:8
5	Tyr L:140	-	Pro L:141

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_066403	W	41	R	IGKC_HUMAN	Disease (IGKCD)	---	L	W	148	R
2	UniProt	VAR_003897	V	84	L	IGKC_HUMAN	Polymorphism	---	L	V	191	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_066403	W	41	R	IGKC_HUMAN	Disease (IGKCD)	---	L	W	148	R
2	UniProt	VAR_003897	V	84	L	IGKC_HUMAN	Polymorphism	---	L	V	191	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_066403	W	41	R	IGKC_HUMAN	Disease (IGKCD)	---	L	W	148	R
2	UniProt	VAR_003897	V	84	L	IGKC_HUMAN	Polymorphism	---	L	V	191	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_066403	W	41	R	IGKC_HUMAN	Disease (IGKCD)	---	L	W	148	R
2	UniProt	VAR_003897	V	84	L	IGKC_HUMAN	Polymorphism	---	L	V	191	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 4 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_066403	W	41	R	IGKC_HUMAN	Disease (IGKCD)	---	L	W	148	R
2	UniProt	VAR_003897	V	84	L	IGKC_HUMAN	Polymorphism	---	L	V	191	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 5 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_066403	W	41	R	IGKC_HUMAN	Disease (IGKCD)	---	L	W	148	R
2	UniProt	VAR_003897	V	84	L	IGKC_HUMAN	Polymorphism	---	L	V	191	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_HUMAN	85-91	1	L:192-198

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_HUMAN	85-91	1	L:192-198

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_HUMAN	85-91	2	L:192-198

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_HUMAN	85-91	2	L:192-198

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_HUMAN	85-91	2	L:192-198

Biological Unit 5 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_HUMAN	85-91	2	L:192-198

(no "Exon" information available for 2NY7)

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 G from PDB  Type:PROTEIN  Length:290
 aligned with ENV_HV1H2 | P04578 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:410
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492
           ENV_HV1H2     83 EVVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVSLKCTDLKNDTNTNSSSGRMIMEKGEIKNCSFNISTSIRGKVQKEYAFFYKLDIIPIDNDTTSYKLTSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSVNFTDNAKTIIVQLNTSVEINCTRPNNNTRKRIRIQRGPGRAFVTIGKIGNMRQAHCNISRAKWNNTLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFNSTWFNSTWSTEGSNNTEGSDTITLPCRIKQIINMWQKVGKAMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVKIE  492
               SCOP domains d2ny7g_ G: automated matches                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains GP120-2ny7G01 G:83-492                                                                                                                                                                                                                                                                                                                                                                                                     Pfam domains
         Sec.struct. author ........eeee............hhhh.eee......-----------------------------------------------------------------------------------......eee..........eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeee..-----------------------------.eeeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhh.eee......--------...eeeeeeeeeeeeeee....eeeee........eeeeeeeeeeee........eeeeee.....hhhhhh....eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ny7 G   83 EVVLVNVTENFNWCKNDMVEQMHEDICSLWDQSLKPCV-----------------------------------------------------------------------------------ACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSSQLLLNGSLAEEEVVIRSCNFTDNAKTIIVQLNTSVEINCTGA-----------------------------GHCNIARAKWNNTLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHWFNCGGEFFYCNSTQLFNSTWFNSTWS--------GSDTITLPCRIKQIINMWCKVGKMMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVKIE  492
                                    92       102       112       | -         -         -         -         -         -         -         -         - |     212       222       232       242       252       262       272       282       292      |  -         -         -      |332       342       352       362       372       382       392        |-       412       422       432       442       452       462       472       482       492
                                                               120                                                                                 204                                                                                            299                           329                                                                     401      410

Chain G from PDB  Type:PROTEIN  Length:290
 aligned with ENV_HV1Y2 | P35961 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:400
                                                                                                                                                                                                                                                                                                                                             387                                                                                            
                                                                                                                                                                                                                                                                                                                                          386  |                                                                                            
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381    |  389       399       409       419       429       439       449       459       469       479
           ENV_HV1Y2     82 EVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDLRNATNTTSSSWETMEKGEIKNCSFNITTSIRDKVQKEYALFYNLDVVPIDNASYRLISCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLF--TWNDTRKLNNTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE  479
               SCOP domains d2ny7g_ G: automated matches                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains GP120-2ny7G01 G:83-492                                                                                                                                                                                                                                                                                                                                                                                           Pfam domains
         Sec.struct. author ........eeee............hhhh.eee......--------------------------------------------------------------------------------......eee..........eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeee..----------------------------.eeeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhh.eee......--...eeeeeeeeeeeeeee....eeeee........eeeeeeeeeeee........eeeeee.....hhhhhh....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ny7 G   83 EVVLVNVTENFNWCKNDMVEQMHEDICSLWDQSLKPCV--------------------------------------------------------------------------------ACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSSQLLLNGSLAEEEVVIRSCNFTDNAKTIIVQLNTSVEINCTGA----------------------------GHCNIARAKWNNTLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHWFNCGGEFFYCNSTQLFNSTWFNSTWS--GSDTITLPCRIKQIINMWCKVGKMMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVKIE  492
                                    92       102       112       | -         -         -         -         -         -         -         -       205       215       225       235       245       255       265       275       285       295   |     -         -         -  |    336       346       356       366       376       386       396    |  412       422       432       442       452       462       472       482       492
                                                               120                                                                              204                                                                                            299                          329                                                                     401  |                                                                                  
                                                                                                                                                                                                                                                                                                                                                       410

Chain H from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                       
               SCOP domains d2ny7h1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                                 d2ny7h2 H:114-230 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 2ny7H01 H:1-109 Immunoglobulins                                                                                            2ny7H02 H:110-230 Immunoglobulins                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeee.................ee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ny7 H    1 QVQLVQSGAEVKKPGASVKVSCQASGYRFSNFVIHWVRQAPGQRFEWMGWINPYNGNKEFSAKFQDRVTFTADTSANTAYMELRSLRSADTAVYYCARVGPYSWDDSPQDNYYMDVWGKGTTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSC  230
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||   106       116       126   ||  138       148     ||163     ||174     ||185       195    |||208       218   ||  230
                                                                              52A                            82A||               100A|||||100J                           130|                  154|||    169|      180|               200||              222|     
                                                                                                              82B|                100B|||||||                             133                   156||     171       182                203|               225     
                                                                                                               82C                 100C||||||                                                    157|                                   205                       
                                                                                                                                    100D|||||                                                     162                                                             
                                                                                                                                     100E||||                                                                                                                     
                                                                                                                                      100F|||                                                                                                                     
                                                                                                                                       100G||                                                                                                                     
                                                                                                                                        100H|                                                                                                                     
                                                                                                                                         100I

Chain L from PDB  Type:PROTEIN  Length:215
 aligned with IGKC_HUMAN | P01834 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:215
                                                                                                                                        1                                                                                                          
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102     
          IGKC_HUMAN      - ------------------------------------------------------------------------------------------------------------RTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  107
               SCOP domains d2ny7l1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                  d2ny7l2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 2ny7L01 L:1-107 Immunoglobulins                                                                             2ny7L02 L:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------R------------------------------------------L----------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ny7 L    1 EIVLTQSPGTLSLSPGERATFSCRSSHSIRSRRVAWYQHKPGQAPRLVIHGVSNRASGISDRFSGSGSGTDFTLTITRVEPEDFALYYCQVYGASSYTFGQGTKLERKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC  214
                                    10        20        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209     
                                                      28A

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: hxbc2. (13)

1a	2ny7L02	L:108-211
1b	2ny7L01	L:1-107
1c	2ny7H02	H:110-230
1d	2ny7H01	H:1-109

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: GP120] (26)

Family: GP120 (26)

Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) (HIV-1) (2)

GP120-2ny7G01

G:83-492

Asymmetric Unit(hide GO term definitions)

Chain G (ENV_HV1Y2 | P35961)

molecular function
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
	GO:0075512	clathrin-dependent endocytosis of virus by host cell	Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0039654	fusion of virus membrane with host endosome membrane	Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
	GO:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0039663	membrane fusion involved in viral entry into host cell	Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
	GO:0002223	stimulatory C-type lectin receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019082	viral protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0044174	host cell endosome	A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
	GO:0044175	host cell endosome membrane	The lipid bilayer surrounding a host cell endosome.
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019031	viral envelope	The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Chain G (ENV_HV1H2 | P04578)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
	GO:0090527	actin filament reorganization	A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of actin filaments.
	GO:0075512	clathrin-dependent endocytosis of virus by host cell	Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0030260	entry into host cell	The invasion by an organism of a cell of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0039654	fusion of virus membrane with host endosome membrane	Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
	GO:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0039663	membrane fusion involved in viral entry into host cell	Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
	GO:1903905	positive regulation of establishment of T cell polarity	Any process that activates or increases the frequency, rate or extent of establishment of T cell polarity.
	GO:1903908	positive regulation of plasma membrane raft polarization	Any process that activates or increases the frequency, rate or extent of plasma membrane raft polarization.
	GO:1903911	positive regulation of receptor clustering	Any process that activates or increases the frequency, rate or extent of receptor clustering.
	GO:0002223	stimulatory C-type lectin receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0019058	viral life cycle	A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019082	viral protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
	GO:0019068	virion assembly	A late phase of the viral life cycle during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0044174	host cell endosome	A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
	GO:0044175	host cell endosome membrane	The lipid bilayer surrounding a host cell endosome.
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019031	viral envelope	The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Chain L (IGKC_HUMAN | P01834)

molecular function
	GO:0003823	antigen binding	Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
	GO:0034987	immunoglobulin receptor binding	Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0050853	B cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
	GO:0038095	Fc-epsilon receptor signaling pathway	A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
	GO:0038096	Fc-gamma receptor signaling pathway involved in phagocytosis	An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
	GO:0006956	complement activation	Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
	GO:0006958	complement activation, classical pathway	Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0006911	phagocytosis, engulfment	The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
	GO:0006910	phagocytosis, recognition	The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
	GO:0050871	positive regulation of B cell activation	Any process that activates or increases the frequency, rate or extent of B cell activation.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0006898	receptor-mediated endocytosis	An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
	GO:0050776	regulation of immune response	Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
	GO:0001895	retina homeostasis	A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
cellular component
	GO:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0042571	immunoglobulin complex, circulating	An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	2ny7
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	IGKC_HUMAN \| P01834
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1hzh	STRUCTURE OF IGG B12

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 13)

Sites (13, 13)

SS Bonds (13, 13)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (1, 1)

Exons (0, 0)

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SCOP Domains (5, 5)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

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