2I60 - 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)

Title :   CRYSTAL STRUCTURE OF [PHE23]M47, A SCORPION-TOXIN MIMIC OF CD4, IN COMPLEX WITH HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN AND ANTI-HIV-1 ANTIBODY 17B

Authors :   C. -C. Huang, P. D. Kwong

Date :   26 Aug 06 (Deposition) - 10 Oct 06 (Release) - 06 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : G,H,L,M,P,Q,R,S
Biol. Unit 1: G,H,L,M  (1x)
Biol. Unit 2: P,Q,R,S  (1x)

Keywords :   Hiv-1, Gp120, Yu2, Scorpion Toxin, Cd4 Mimic, [Phe23]M47, Antibody, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Stricher, C. C. Huang, A. Descours, S. Duquesnoy, O. Combes, J. M. Decker, Y. D. Kwon, P. Lusso, G. M. Shaw, C. Vita, P. D. Kwong, L. Martin
Combinatorial Optimization Of A Cd4-Mimetic Miniprotein And Cocrystal Structures With Hiv-1 Gp120 Envelope Glycoprotein
J. Mol. Biol. V. 382 510 2008
PubMed-ID: 18619974 | Reference-DOI: 10.1016/J.JMB.2008.06.069

Molecule 1 - EXTERIOR MEMBRANE GLYCOPROTEIN(GP120)
	Chains	:	G, P
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Common	:	FRUIT FLY
	Expression System Taxid	:	7227
	Fragment	:	CORE
	Gene	:	ENV
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676
	Strain	:	YU2
	Synonym	:	HIV-1 YU2 GP120

Molecule 2 - ANTIBODY 17B LIGHT CHAIN
	Chains	:	L, Q
	Engineered	:	YES
	Expression System	:	HUMAN HERPESVIRUS 4
	Expression System Common	:	EPSTEIN-BARR VIRUS
	Expression System Taxid	:	10376
	Fragment	:	ANTIGEN-BINDING FRAGMENT, FAB
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - ANTIBODY 17B HEAVY CHAIN
	Chains	:	H, R
	Engineered	:	YES
	Expression System	:	HUMAN HERPESVIRUS 4
	Expression System Common	:	EPSTEIN-BARR VIRUS
	Expression System Taxid	:	10376
	Fragment	:	ANTIGEN-BINDING FRAGMENT, FAB
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 4 - [PHE23]M47, SCORPION-TOXIN MIMIC OF CD4
	Chains	:	M, S
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Other Details	:	THIS PROTEIN IS A MIMIC OF THE PROTEIN THAT OCCURS NATURALLY IN LEIURUS QUINQUESTRIATUS HEBRAEUS (ISRAELI SCORPION)
	Synthetic	:	YES

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	G	H	L	M	P	Q	R	S
Biological Unit 1 (1x)	:	G	H	L	M
Biological Unit 2 (1x)	:					P	Q	R	S

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 24)

No.	Name	Count	Type	Full Name
1	DPR	2	Mod. Amino Acid	D-PROLINE
2	IPA	2	Ligand/Ion	ISOPROPYL ALCOHOL
3	MPT	2	Mod. Amino Acid	BETA-MERCAPTOPROPIONIC ACID
4	NAG	12	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NDG	4	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6	VLM	2	Mod. Amino Acid	VALINYLAMINE

Biological Unit 1 (6, 12)

No.	Name	Count	Type	Full Name
1	DPR	1	Mod. Amino Acid	D-PROLINE
2	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
3	MPT	1	Mod. Amino Acid	BETA-MERCAPTOPROPIONIC ACID
4	NAG	7	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6	VLM	1	Mod. Amino Acid	VALINYLAMINE

Biological Unit 2 (6, 12)

No.	Name	Count	Type	Full Name
1	DPR	1	Mod. Amino Acid	D-PROLINE
2	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
3	MPT	1	Mod. Amino Acid	BETA-MERCAPTOPROPIONIC ACID
4	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NDG	3	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6	VLM	1	Mod. Amino Acid	VALINYLAMINE

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN G:88 , ASN G:241 , HOH G:955	BINDING SITE FOR RESIDUE NAG G 588
02	AC2	SOFTWARE	ASN G:234 , THR G:236	BINDING SITE FOR RESIDUE NAG G 734
03	AC3	SOFTWARE	ASP G:230 , LYS G:231 , THR G:240 , ASN G:241	BINDING SITE FOR RESIDUE NAG G 741
04	AC4	SOFTWARE	VAL G:254 , ASN G:262 , ASN G:377 , CYS G:378 , SER G:446 , SER G:447 , HOH G:933	BINDING SITE FOR RESIDUE NAG G 762
05	AC5	SOFTWARE	ASN G:276 , THR G:278 , ASN G:279	BINDING SITE FOR RESIDUE NAG G 776
06	AC6	SOFTWARE	GLU G:268 , GLU G:269 , ILE G:270 , ASN G:289 , GLU G:290 , GLN G:344 , LYS G:348 , HOH G:902 , LYS L:188	BINDING SITE FOR RESIDUE NAG G 789
07	AC7	SOFTWARE	GLU G:87 , ASN G:295	BINDING SITE FOR RESIDUE NAG G 795
08	AC8	SOFTWARE	ASN G:386 , THR G:388 , HOH G:895 , GLY S:14 , LEU S:15	BINDING SITE FOR RESIDUE NDG G 886
09	AC9	SOFTWARE	SER G:375 , PHE G:376 , ASN G:377 , TYR G:384	BINDING SITE FOR RESIDUE IPA G 501
10	BC1	SOFTWARE	ASN P:88 , THR P:240 , ASN P:241 , NDG P:741 , HOH P:930 , HOH P:931	BINDING SITE FOR RESIDUE NAG P 588
11	BC2	SOFTWARE	ASN P:234	BINDING SITE FOR RESIDUE NDG P 734
12	BC3	SOFTWARE	ASP P:230 , LYS P:231 , ASN P:241 , NAG P:588	BINDING SITE FOR RESIDUE NDG P 741
13	BC4	SOFTWARE	ASN P:262 , ASN P:377 , CYS P:378 , SER P:446 , SER P:447	BINDING SITE FOR RESIDUE NAG P 762
14	BC5	SOFTWARE	LYS G:460 , ASN P:276 , THR P:278 , ASN P:279 , HOH P:907	BINDING SITE FOR RESIDUE NAG P 776
15	BC6	SOFTWARE	GLU P:267 , GLU P:268 , GLU P:269 , ILE P:270 , ASN P:289 , GLU P:290 , GLN P:344 , LYS Q:190	BINDING SITE FOR RESIDUE NDG P 789
16	BC7	SOFTWARE	GLU P:87 , ASN P:295	BINDING SITE FOR RESIDUE NAG P 795
17	BC8	SOFTWARE	HOH M:246 , ASN P:386 , THR P:388 , HOH P:938	BINDING SITE FOR RESIDUE NAG P 886
18	BC9	SOFTWARE	VAL P:255 , SER P:256 , SER P:375 , PHE P:376 , PHE P:382 , MET P:475 , HOH P:923	BINDING SITE FOR RESIDUE IPA P 502

Asymmetric Unit

No.	Residues
1	G:119	-	G:205
2	G:126	-	G:196
3	G:218	-	G:247
4	G:228	-	G:239
5	G:296	-	G:331
6	G:378	-	G:445
7	G:385	-	G:418
8	H:22	-	H:92
9	H:140	-	H:196
10	L:23	-	L:88
11	L:134	-	L:194
12	M:6	-	M:24
13	M:10	-	M:26
14	P:119	-	P:205
15	P:126	-	P:196
16	P:218	-	P:247
17	P:228	-	P:239
18	P:296	-	P:331
19	P:378	-	P:445
20	P:385	-	P:418
21	Q:23	-	Q:88
22	Q:134	-	Q:194
23	R:22	-	R:92
24	R:140	-	R:196
25	S:6	-	S:24
26	S:10	-	S:26

Asymmetric Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Trp L:94	-	Pro L:95
3	Tyr L:140	-	Pro L:141
4	Phe H:146	-	Pro H:147
5	Glu H:148	-	Pro H:149
6	Ser Q:7	-	Pro Q:8
7	Trp Q:94	-	Pro Q:95
8	Tyr Q:140	-	Pro Q:141
9	Phe R:146	-	Pro R:147
10	Glu R:148	-	Pro R:149

(no "SAP(SNP)/Variant" information available for 2I60)

(no "PROSITE Motif" information available for 2I60)

(no "Exon" information available for 2I60)

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:301
 aligned with ENV_HV1Y2 | P35961 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:398
                                    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       391       401       411       421       431       441       451       461       471        
           ENV_HV1Y2     82 EVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDLRNATNTTSSSWETMEKGEIKNCSFNITTSIRDKVQKEYALFYNLDVVPIDNASYRLISCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE  479
               SCOP domains d2i60g_ G: gp120 core                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2i60G00 G:83-492 HIV Envelope Protein Gp120; Ch                                                             ain G                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee...hhhhhhhhhhhhhhhhhhh...eeeeeee...-------------------------------------------------------------..eeeeeee....................eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeee..----------------------------.eeeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhh.ee.--------.eeeeeeeee.eee......eee..........eeeeeeeeeeee........eeeeee....hhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2i60 G   83 EVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVGA-------------------------------------------------------------GSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTGA----------------------------GHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWND--------RNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE  492
                                    92       102       112       122      |  -         -         -         -         -         -       195       205       215       225       235       245       255       265       275       285       295   |     -         -         -  |    336       346       356       366       376       386        |-       414       424       434       444       454       464       474       484        
                                                                        129                                                           194                                                                                                      299                          329                                                               395      412

Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains d2i60h1 H:2-113 Immunoglobulin heavy chain variable domain, VH                                                                 d2i60h2 H:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                SCOP domains
               CATH domains 2i60H01 H:2-113 Immunoglobulins                                                                                                2i60H02 H:114-213 Immunoglobulins                                                            - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee..hhh.eeeeeeee......eeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..hhhhh.........ee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2i60 H    2 VQLVESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHYAPHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQGTLVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    11        21        31        41        51 |      60        70        80  ||||  87        97   |||100G||||   106       116       126|      143       153       163       173       183       193       203       213 
                                                                             52A                            82A|||              100A|||||100J|                       126|                                                                                
                                                                                                             82B||               100B|||||100K                        134                                                                                
                                                                                                              85C|                100C||||||                                                                                                             
                                                                                                                83                 100D|||||                                                                                                             
                                                                                                                                    100E||||                                                                                                             
                                                                                                                                     100F|||                                                                                                             
                                                                                                                                      100G||                                                                                                             
                                                                                                                                       100H|                                                                                                             
                                                                                                                                        100I

Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d2i60l1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                   d2i60l2 L:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 2i60L01 L:1-108 Immunoglobulins                                                                               2i60L02 L:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee........ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2i60 L    1 DIVMTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPARFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20        30        40        50        60        70        80        90     || 98       108       118       128       138       148       158       168       178       188       198       208    
                                                                                                                         95A|                                                                                                                     
                                                                                                                          95B

Chain M from PDB  Type:PROTEIN  Length:27
                                                            
               SCOP domains -d2i60m1 M:2-27             SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eeeee..eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                2i60 M    1 xNLHFCQLRCKSLGLLGRCAxTFCACx   27
                            |       10        20|     |
                            1-MPT              21-DPR |
                                                     27-VLM

Chain P from PDB  Type:PROTEIN  Length:300
 aligned with ENV_HV1Y2 | P35961 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:399
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470         
           ENV_HV1Y2     81 QEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDLRNATNTTSSSWETMEKGEIKNCSFNITTSIRDKVQKEYALFYNLDVVPIDNASYRLISCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE  479
               SCOP domains d2i60p_ P: gp120 core                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2i60P00 P:82-492 HIV Envelope Protein Gp120; Cha                                                             in G                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee...hhhhhhhhhhhhhhhh......eeeeee....-------------------------------------------------------------...eeeeee....................eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeee...----------------------------.eeeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhh..----------.eeeeeeeee.eee......eee..........eeeeeeeeeeeee.......eeeeee....hhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2i60 P   82 SEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVGA-------------------------------------------------------------GSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTGA----------------------------GHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTW----------RNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE  492
                                    91       101       111       121       | -         -         -         -         -         -       194       204       214       224       234       244       254       264       274       284       294    |    -         -         -   |   335       345       355       365       375       385       | -       413       423       433       443       453       463       473       483         
                                                                         129                                                           194                                                                                                      299                          329                                                             393        412

Chain Q from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d2i60q1 Q:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                   d2i60q2 Q:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 2i60Q01 Q:1-108 Immunoglobulins                                                                               2i60Q02 Q:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee........ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2i60 Q    1 DIVMTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPARFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20        30        40        50        60        70        80        90     || 98       108       118       128       138       148       158       168       178       188       198       208    
                                                                                                                         95A|                                                                                                                     
                                                                                                                          95B

Chain R from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains d2i60r1 R:1-113 Immunoglobulin heavy chain variable domain, VH                                                                  d2i60r2 R:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                SCOP domains
               CATH domains 2i60R01 R:1-113 Immunoglobulins                                                                                                 2i60R02 R:114-213 Immunoglobulins                                                            - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhh.eeeeeeee......eeeeee.hhhh.eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..hhhhh.........ee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2i60 R    1 EVQLVESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHYAPHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQGTLVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||||  105       115       125||     142       152       162       172       182       192       202       212  
                                                                              52A                            82A||               100A|||||100J|                       126|                                                                                
                                                                                                              82B|                100B|||||100K                        134                                                                                
                                                                                                               82C                 100C||||||                                                                                                             
                                                                                                                                    100D|||||                                                                                                             
                                                                                                                                     100E||||                                                                                                             
                                                                                                                                      100F|||                                                                                                             
                                                                                                                                       100G||                                                                                                             
                                                                                                                                        100H|                                                                                                             
                                                                                                                                         100I

Chain S from PDB  Type:PROTEIN  Length:27
                                                            
               SCOP domains -d2i60s1 S:2-27             SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eeeee..eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                2i60 S    1 xNLHFCQLRCKSLGLLGRCAxTFCACx   27
                            |       10        20|     |
                            1-MPT              21-DPR |
                                                     27-VLM

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: Beta Complex (381)

Topology: HIV Envelope Protein Gp120; Chain G (17)

Homologous Superfamily: HIV Envelope Protein Gp120; Chain G (17)

Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: yu2. (1)

1a	2i60G00	G:83-492
1b	2i60P00	P:82-492

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: yu2. (2)

2a	2i60L02	L:109-211
2b	2i60Q02	Q:109-211
2c	2i60H01	H:2-113
2d	2i60R01	R:1-113
2e	2i60L01	L:1-108
2f	2i60Q01	Q:1-108
2g	2i60H02	H:114-213
2h	2i60R02	R:114-213

(no "Pfam Domain" information available for 2I60)

Asymmetric Unit(hide GO term definitions)

Chain G,P (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.

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	2i60
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1yyl	CRYSTAL STRUCTURE OF CD4M33, A SCORPION-TOXIC MIMIC OF CD4, IN COMPLEX WITH HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN AND ANTI-HIV-1 ANTIBODY 17B
1yym	CRYSTAL STRUCTURE OF F23, A SCORPION-TOXIN MIMIC OF CD4, IN COMPLEX WITH HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN AND ANTI -HIV-1 ANTIBODY 17B
2i5y	CRYSTAL STRUCTURE OF CD4M47, A SCORPION-TOXIN MIMIC OF CD4, IN COMPLEX WITH HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN AND ANTI-HIV-1 ANTIBODY 17B

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 24)

Sites (18, 18)

SS Bonds (26, 26)

Cis Peptide Bonds (10, 10)

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SCOP Domains (6, 12)

CATH Domains (2, 10)

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Gene Ontology (21, 21)

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