1RZG - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN ANTI-HIV-1 GP120 REACTIVE ANTIBODY 412D

Authors :   C. C. Huang, M. Venturi, S. Majeed, M. J. Moore, S. Phogat, M. -Y. Zhang, D. S. Dimitrov, W. A. Hendrickson, J. Robinson, J. Sodroski, R. Wyatt, H. Choe, M. Farzan, P. D. Kwong

Date :   24 Dec 03 (Deposition) - 03 Feb 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Hiv-1; Gp120; Cd4I; Antibodies; Tyrosine Sulfation; Vh-Gene Usage, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. C. Huang, M. Venturi, S. Majeed, M. J. Moore, S. Phogat, M. -Y. Zhang, D. S. Dimitrov, W. A. Hendrickson, J. Robinson, J. Sodroski, R. Wyatt, H. Choe, M. Farzan, P. D. Kwong
Structural Basis Of Tyrosine Sulfation And Vh-Gene Usage In Antibodies That Recognize The Hiv Type 1 Coreceptor-Binding Site On Gp120
Proc. Natl. Acad. Sci. Usa V. 101 2706 2004
PubMed-ID: 14981267 | Reference-DOI: 10.1073/PNAS.0308527100
(for further references see the PDB file header)

Molecule 1 - FAB 412D LIGHT CHAIN
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	HUMAN HERPESVIRUS 4
	Expression System Cell	:	IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER
	Expression System Common	:	EPSTEIN-BARR VIRUS
	Expression System Taxid	:	10376
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - FAB 412D HEAVY CHAIN
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	HUMAN HERPESVIRUS 4
	Expression System Cell	:	IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER
	Expression System Common	:	EPSTEIN-BARR VIRUS
	Expression System Taxid	:	10376
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 11)

No.	Name	Count	Type	Full Name
1	ASP	1	Mod. Amino Acid	ASPARTIC ACID
2	CYS	1	Mod. Amino Acid	CYSTEINE
3	SUC	7	Ligand/Ion	SUCROSE
4	TYS	2	Mod. Amino Acid	O-SULFO-L-TYROSINE

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	ASP	-1	Mod. Amino Acid	ASPARTIC ACID
2	CYS	-1	Mod. Amino Acid	CYSTEINE
3	SUC	4	Ligand/Ion	SUCROSE
4	TYS	1	Mod. Amino Acid	O-SULFO-L-TYROSINE

Biological Unit 2 (4, 6)

No.	Name	Count	Type	Full Name
1	ASP	1	Mod. Amino Acid	ASPARTIC ACID
2	CYS	1	Mod. Amino Acid	CYSTEINE
3	SUC	3	Ligand/Ion	SUCROSE
4	TYS	1	Mod. Amino Acid	O-SULFO-L-TYROSINE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:59 , GLN A:64 , GLY A:65 , ARG A:66 , VAL A:67 , SER A:68 , SUC A:9005 , HOH A:9012 , HOH A:9014 , HOH A:9029 , HOH A:9061	BINDING SITE FOR RESIDUE SUC A 9001
2	AC2	SOFTWARE	ARG A:38 , GLN A:43 , GLY A:44 , LEU A:45 , GLU A:46 , ARG A:62 , HOH A:9009 , HOH A:9010 , HOH A:9035 , HOH A:9145 , HOH A:9167 , THR B:97 , PHE B:98 , GLN B:100 , HOH B:278	BINDING SITE FOR RESIDUE SUC A 9002
3	AC3	SOFTWARE	ARG C:38 , GLN C:43 , GLY C:44 , LEU C:45 , GLU C:46 , HOH C:9009 , THR D:97 , PHE D:98 , GLN D:100 , HOH D:9020 , HOH D:9033 , HOH D:9041	BINDING SITE FOR RESIDUE SUC D 9003
4	AC4	SOFTWARE	TYR C:59 , GLN C:64 , GLY C:65 , ARG C:66 , VAL C:67 , SER C:68 , SUC C:9006 , HOH C:9016 , HOH C:9093	BINDING SITE FOR RESIDUE SUC C 9004
5	AC5	SOFTWARE	ASN A:55 , SER A:68 , ILE A:69 , THR A:70 , SUC A:9001 , HOH A:9012 , HOH A:9014 , HOH A:9033 , HOH A:9103 , HOH A:9134	BINDING SITE FOR RESIDUE SUC A 9005
6	AC6	SOFTWARE	ASN C:55 , TYR C:59 , SER C:68 , ILE C:69 , SUC C:9004 , HOH C:9016	BINDING SITE FOR RESIDUE SUC C 9006
7	AC7	SOFTWARE	GLY A:100H , MET A:100I , SER A:100J , TRP A:100K , HOH A:9066 , TRP B:32 , LYS B:50 , HIS B:91 , ASP B:92 , HOH B:389	BINDING SITE FOR RESIDUE SUC A 9007
8	AC8	SOFTWARE	CYS D:214 , ASP D:9005 , HOH D:9161	BINDING SITE FOR RESIDUE CYS D 9004
9	AC9	SOFTWARE	CYS D:9004 , HOH D:9122 , HOH D:9130 , HOH D:9161	BINDING SITE FOR RESIDUE ASP D 9005

Asymmetric Unit

No.	Residues
1	A:22	-	A:92
2	A:140	-	A:196
3	B:23	-	B:88
4	B:134	-	B:194
5	C:22	-	C:92
6	C:140	-	C:196
7	D:23	-	D:88
8	D:134	-	D:194
9	D:214	-	D:9004

Asymmetric Unit

No.	Residues
1	Phe A:146	-	Pro A:147
2	Glu A:148	-	Pro A:149
3	Ser B:7	-	Pro B:8
4	Ser B:94	-	Pro B:95
5	Tyr B:140	-	Pro B:141
6	Phe C:146	-	Pro C:147
7	Glu C:148	-	Pro C:149
8	Ser D:7	-	Pro D:8
9	Ser D:94	-	Pro D:95
10	Tyr D:140	-	Pro D:141

(no "SAP(SNP)/Variant" information available for 1RZG)

(no "PROSITE Motif" information available for 1RZG)

(no "Exon" information available for 1RZG)

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:224
                                                                                                                                                                                                                                                                 
               SCOP domains d1rzga1 A:1-113 Immunoglobulin heavy chain variable domain, VH                                                             d1rzga2 A:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1rzgA01 A:1-109 Immunoglobulins                                                                                        1rzgA02 A:110-214 Immunoglobulins                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...eee.....eeeeee....hhhhh.eeeeee......eeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeee.............ee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rzg A    1 EVQLVQSGAEVKKPGSSVKVSCKASGGTFSNYAINWVRQAPGQGLEWMGGIIPIFNIAHYAQRFQGRVSITADESTSTAYMELSSLRSEDTAVFYCASPYPNDyGMSWYFDLWGRGTLVTVSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96   |||100M       110       120       130       140       150       160       170       180       190       200       210    
                                                                              52A                            82A||               100-TYS||                                                                                                                  
                                                                                                              82B|               100H|||||                                                                                                                  
                                                                                                               82C                100I||||                                                                                                                  
                                                                                                                                   100J|||                                                                                                                  
                                                                                                                                    100K||                                                                                                                  
                                                                                                                                     100L|                                                                                                                  
                                                                                                                                      100M

Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d1rzgb1 B:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1rzgb2 B:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1rzgB01 B:1-108 Immunoglobulins                                                                             -1rzgB02 B:110-211 Immunoglobulins                                                                     -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rzg B    1 DIQMTQSPSTLSASVGDRVTITCRASQSISNWLAWYQQKPGRAPKLLMYKASSLKSGVPSRFSGSGSGTEFTLTISSLQSDDFATYYCQQHDSSPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKLYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain C from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d1rzgc1 C:2-113 Immunoglobulin heavy chain variable domain, VH                                                            d1rzgc2 C:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma              SCOP domains
               CATH domains 1rzgC01 C:2-109 Immunoglobulins                                                                                       1rzgC02 C:110-213 Immunoglobulins                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee.....eeeeeee...hhhhh.eeeeee......eeeeeee....eeee.hhhh..eeeeee....eeeeee........eeeeeee.............ee...eeeee........eeeee...eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee.hhhhhh...eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rzg C    2 VQLVQSGAEVKKPGSSVKVSCKASGGTFSNYAINWVRQAPGQGLEWMGGIIPIFNIAHYAQRFQGRVSITADESTSTAYMELSSLRSEDTAVFYCASPYPNDyGMSWYFDLWGRGTLVTVSPASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    11        21        31        41        51 |      60        70        80  |||   87        97  |||||101       111       121    || 139       149       159       169       179       189       199       209    
                                                                             52A                            82A||               100-TYS||                       126|                                                                              
                                                                                                             82B|               100H|||||                        135                                                                              
                                                                                                              82C                100I||||                                                                                                         
                                                                                                                                  100J|||                                                                                                         
                                                                                                                                   100K||                                                                                                         
                                                                                                                                    100L|                                                                                                         
                                                                                                                                     100M

Chain D from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d1rzgd1 D:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1rzgd2 D:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1rzgD01 D:1-108 Immunoglobulins                                                                             -1rzgD02 D:110-211 Immunoglobulins                                                                     --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee...........eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rzg D    1 DIQMTQSPSTLSASVGDRVTITCRASQSISNWLAWYQQKPGRAPKLLMYKASSLKSGVPSRFSGSGSGTEFTLTISSLQSDDFATYYCQQHDSSPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKLYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 (Homo sapiens) (912)

1a	1rzgB02	B:110-211
1b	1rzgA02	A:110-214
1c	1rzgC02	C:110-213
1d	1rzgC01	C:2-109
1e	1rzgA01	A:1-109
1f	1rzgD02	D:110-211
1g	1rzgB01	B:1-108
1h	1rzgD01	D:1-108

(no "Pfam Domain" information available for 1RZG)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1RZG)

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:148 - Pro A:149	[ RasMol ]
		Glu C:148 - Pro C:149	[ RasMol ]
		Phe A:146 - Pro A:147	[ RasMol ]
		Phe C:146 - Pro C:147	[ RasMol ]
		Ser B:7 - Pro B:8	[ RasMol ]
		Ser B:94 - Pro B:95	[ RasMol ]
		Ser D:7 - Pro D:8	[ RasMol ]
		Ser D:94 - Pro D:95	[ RasMol ]
		Tyr B:140 - Pro B:141	[ RasMol ]
		Tyr D:140 - Pro D:141	[ RasMol ]

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	1rzg
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (4, 11)

Sites (9, 9)

SS Bonds (9, 9)

Cis Peptide Bonds (10, 10)

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SAPs(SNPs)/Variants (0, 0)

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