1ZLV - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   FAB 2G12 + MAN7

Authors :   D. A. Calarese, H. -K. Lee, M. D. Best, R. D. Astronomo, R. L. Stanfield, D. R. Burton, C. H. Wong, I. A. Wilson

Date :   09 May 05 (Deposition) - 09 Aug 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.33

Chains :   Asym./Biol. Unit : H,K,L,M

Keywords :   Hiv Neutralizing Antibody; Anti-Carbohydrate; Domain- Swapping, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. A. Calarese, H. -K. Lee, C. Y. Huang, M. D. Best, R. D. Astronomo, R. L. Stanfield, H. Katinger, D. R. Burton, C. H. Wong, I. A. Wilson
Dissection Of The Carbohydrate Specificity Of The Broadly Neutralizing Anti-Hiv-1 Antibody 2G12
Proc. Natl. Acad. Sci. Usa V. 102 13372 2005
PubMed-ID: 16174734 | Reference-DOI: 10.1073/PNAS.0505763102
(for further references see the PDB file header)

Molecule 1 - FAB 2G12, LIGHT CHAIN
	Chains	:	L, K
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Cell	:	DHFR
	Expression System Common	:	CHINESE HAMSTER
	Expression System Organ	:	OVARY
	Expression System Taxid	:	10029
	Fragment	:	FAB, LIGHT CHAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - FAB 2G12, HEAVY CHAIN
	Chains	:	H, M
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Cell	:	DHFR
	Expression System Common	:	CHINESE HAMSTER
	Expression System Organ	:	OVARY
	Expression System Taxid	:	10029
	Fragment	:	FAB, HEAVY CHAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric/Biological Unit	:	H	K	L	M

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 8)

No.	Name	Count	Type	Full Name
1	MAN	8	Ligand/Ion	ALPHA-D-MANNOSE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA H:31 , HIS H:32 , THR H:33 , LYS H:95 , GLY H:96 , LEU H:100 , SER H:100A , ASP H:100B , ASN H:100C , ASP H:100D , MAN H:230 , GLY L:93	BINDING SITE FOR RESIDUE MAN H 229
2	AC2	SOFTWARE	ALA H:31 , LEU H:100 , SER H:100A , ASP H:100B , MAN H:229 , MAN H:231	BINDING SITE FOR RESIDUE MAN H 230
3	AC3	SOFTWARE	MAN H:230 , MAN H:232 , TYR L:94	BINDING SITE FOR RESIDUE MAN H 231
4	AC4	SOFTWARE	ASP H:100B , MAN H:231	BINDING SITE FOR RESIDUE MAN H 232
5	AC5	SOFTWARE	GLY K:93 , ALA M:31 , HIS M:32 , THR M:33 , LYS M:95 , GLY M:96 , LEU M:100 , SER M:100A , ASP M:100B , ASN M:100C , ASP M:100D , MAN M:230	BINDING SITE FOR RESIDUE MAN M 229
6	AC6	SOFTWARE	ALA M:31 , ASP M:100B , MAN M:229 , MAN M:231 , MAN M:232	BINDING SITE FOR RESIDUE MAN M 230
7	AC7	SOFTWARE	TYR K:94 , ASP M:100B , MAN M:230 , MAN M:232	BINDING SITE FOR RESIDUE MAN M 231
8	AC8	SOFTWARE	ASP M:100B , MAN M:230 , MAN M:231	BINDING SITE FOR RESIDUE MAN M 232

Asymmetric/Biological Unit

No.	Residues
1	H:22	-	H:92
2	H:142	-	H:208
3	K:23	-	K:88
4	K:134	-	K:194
5	L:23	-	L:88
6	L:134	-	L:194
7	M:22	-	M:92
8	M:142	-	M:208

Asymmetric/Biological Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Tyr L:140	-	Pro L:141
3	Phe H:148	-	Pro H:149
4	Glu H:150	-	Pro H:151
5	Ser K:7	-	Pro K:8
6	Tyr K:140	-	Pro K:141
7	Phe M:148	-	Pro M:149
8	Glu M:150	-	Pro M:151

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

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

(no "Exon" information available for 1ZLV)

Asymmetric/Biological 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 H from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d1zlvh1 H:1-112 Immunoglobulin heavy chain variable domain, VH                                                          -d1zlvh2 H:114-227 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma              SCOP domains
               CATH domains 1zlvH01 H:1-113 Immunoglobulins                                                                                          1zlvH02 H:114-227 Immunoglobulins                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeee....eeeeeeee........eeeeee.....eeeeeee.hhhh.eee.......eeeeee....eeeeee...hhhhheeeeeeee........eeee...eeeeee.......eeeee...eeeeeeeeee.....eeee........eee...ee.....eeeeeeeeehhhhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zlv H    1 EVQLVESGGGLVKAGGSLILSCGVSNFRISAHTMNWVRRVPGGGLEWVASISTSSTYRDYADAVKGRFTVSRDDLEDFVYLQMHKMRVEDTAIYYCARKGSLSDNDPFDAWGPGTVVTVSPASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  227
                                    10        20        30        40        50  |     59        69        79   |||  86        96|||||||102       112       122   ||  142       152 ||||  167 ||    178 ||    189       199|||    212       222|  
                                                                              52A                            82A||             97|||||||                       126|              154|||    169|      180|               200||              222|  
                                                                                                              82B|             100||||||                        137               156||     171       182                203|               225  
                                                                                                               82C             100A|||||                                           157|                                   205                    
                                                                                                                                100B||||                                            162                                                          
                                                                                                                                 100C|||                                                                                                         
                                                                                                                                  100D||                                                                                                         
                                                                                                                                   100E|                                                                                                         
                                                                                                                                    100F

Chain K from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains d1zlvk1 K:2-107 automated matches                                                                         d1zlvk2 K:108-212 automated matches                                                                       SCOP domains
               CATH domains 1zlvK01 K:2-107 Immunoglobulins                                                                           1zlvK02 K:108-212 Immunoglobulins                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee....eeeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeeee....eee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zlv K    2 VVMTQSPSTLSASVGDTITITCRASQSIETWLAWYQQKPGKAPKLLIYKASTLKTGVPSRFSGSGSGTEFTLTISGLQFDDFATYHCQHYAGYSATFGQGTRVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains d1zlvl1 L:2-107 automated matches                                                                         d1zlvl2 L:108-212 automated matches                                                                       SCOP domains
               CATH domains 1zlvL01 L:2-107 Immunoglobulins                                                                           1zlvL02 L:108-212 Immunoglobulins                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee....eeeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeeee..hhhhh.eeeeeeee..eeee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zlv L    2 VVMTQSPSTLSASVGDTITITCRASQSIETWLAWYQQKPGKAPKLLIYKASTLKTGVPSRFSGSGSGTEFTLTISGLQFDDFATYHCQHYAGYSATFGQGTRVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain M from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains d1zlvm1 M:1-112 Immunoglobulin heavy chain variable domain, VH                                                            -d1zlvm2 M:114-227 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                SCOP domains
               CATH domains 1zlvM01 M:1-113 Immunoglobulins                                                                                            1zlvM02 M:114-227 Immunoglobulins                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeee....eeeeeeee........eeeeee.....eeeeeee.hhhh.eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee..........eeee...eeeeee.......eeeee.......eeeeeeeeeee.....eeee.....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zlv M    1 EVQLVESGGGLVKAGGSLILSCGVSNFRISAHTMNWVRRVPGGGLEWVASISTSSTYRDYADAVKGRFTVSRDDLEDFVYLQMHKMRVEDTAIYYCARKGSDRLSDNDPFDAWGPGTVVTVSPASTKGPSVFPLAPSTSGGTAALGCLVKDYFPEPVTVSWNLTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  227
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F       110       120      |135       145       156|||  ||174     ||185       195    |||208       218   ||  
                                                                              52A                            82A||               100A|||||                        127|                  154||||  ||      180|               200||              222|  
                                                                                                              82B|                100B||||                         133                   156|||  ||       182                203|               225  
                                                                                                               82C                 100C|||                                                157||  ||                           205                    
                                                                                                                                    100D||                                                 162|  ||                                                  
                                                                                                                                     100E|                                                  166  ||                                                  
                                                                                                                                      100F                                                     169|                                                  
                                                                                                                                                                                                171

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/Biological 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	1zlvK02	K:108-212
1b	1zlvM02	M:114-227
1c	1zlvH02	H:114-227
1d	1zlvH01	H:1-113
1e	1zlvM01	M:1-113
1f	1zlvL02	L:108-212
1g	1zlvK01	K:2-107
1h	1zlvL01	L:2-107

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

Asymmetric/Biological Unit(hide GO term definitions)

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

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu H:150 - Pro H:151	[ RasMol ]
		Glu M:150 - Pro M:151	[ RasMol ]
		Phe H:148 - Pro H:149	[ RasMol ]
		Phe M:148 - Pro M:149	[ RasMol ]
		Ser K:7 - Pro K:8	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Tyr K:140 - Pro K:141	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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	1zlv
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (8, 8)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (4, 8)

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