4JO2 - JenaLib

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Title :   CRYSTAL STRUCTURE OF RABBIT MAB R56 FAB IN COMPLEX WITH V3 CROWN OF HIV-1 CONSENSUS A GP120

Authors :   R. M. Pan, X. P. Kong

Date :   16 Mar 13 (Deposition) - 31 Jul 13 (Release) - 04 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Ig, Antibody, Immune System-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Pan, J. M. Sampson, Y. Chen, M. Vaine, S. Wang, S. Lu, X. P. Kong
Rabbit Anti-Hiv-1 Monoclonal Antibodies Raised By Immunization Can Mimic The Antigen-Binding Modes Of Antibodies Derived From Hiv-1-Infected Humans.
J. Virol. V. 87 10221 2013
PubMed-ID: 23864637 | Reference-DOI: 10.1128/JVI.00843-13

Molecule 1 - MONOCLONAL ANTI-HIV-1 GP120 V3 ANTIBODY R56 LIGHT CHAIN
	Chains	:	L, M
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Fragment	:	FAB
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986

Molecule 2 - MONOCLONAL ANTI-HIV-1 GP120 V3 ANTIBODY R56 HEAVY CHAIN
	Chains	:	H, I
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Fragment	:	FAB
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986

Molecule 3 - GP120
	Chains	:	P, Q
	Engineered	:	YES
	Fragment	:	THIRD VARIABLE REGION (V3) CROWN (UNP RESIDUES 30-52)
	Gene	:	ENV
	Organism Common	:	HIV-1
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676

		1	2	3	4	5	6
Asymmetric Unit	:	H	I	L	M	P	Q
Biological Unit 1 (1x)	:	H		L		P
Biological Unit 2 (1x)	:		I		M		Q

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP H:47 , PHE L:98	BINDING SITE FOR RESIDUE CA L 301
2	AC2	SOFTWARE	PRO L:8 , SER L:9	BINDING SITE FOR RESIDUE CA L 302
3	AC3	SOFTWARE	TYR H:59	BINDING SITE FOR RESIDUE CA H 301
4	AC4	SOFTWARE	TRP I:47 , PHE M:98	BINDING SITE FOR RESIDUE CA M 301
5	AC5	SOFTWARE	PRO M:8 , SER M:9	BINDING SITE FOR RESIDUE CA M 302
6	AC6	SOFTWARE	TYR I:59	BINDING SITE FOR RESIDUE CA I 301

Asymmetric Unit

No.	Residues
1	H:22	-	H:92
2	H:35A	-	H:50
3	H:136	-	H:189
4	I:22	-	I:92
5	I:35A	-	I:50
6	I:136	-	I:189
7	L:23	-	L:88
8	L:80	-	L:170
9	L:94	-	L:95D
10	L:134	-	L:193
11	L:211	-	H:123
12	M:23	-	M:88
13	M:80	-	M:170
14	M:94	-	M:95D
15	M:134	-	M:193
16	M:211	-	I:123

Asymmetric Unit

No.	Residues
1	Thr L:7	-	Pro L:8
2	Phe L:140	-	Pro L:141
3	Leu H:142	-	Pro H:143
4	Glu H:144	-	Pro H:145
5	Ser H:183	-	Ser H:184
6	Ser H:184	-	Gln H:185
7	Thr M:7	-	Pro M:8
8	Phe M:140	-	Pro M:141
9	Leu I:142	-	Pro I:143
10	Glu I:144	-	Pro I:145
11	Ser I:182	-	Ser I:183

(no "SAP(SNP)/Variant" information available for 4JO2)

(no "PROSITE Motif" information available for 4JO2)

(no "Exon" information available for 4JO2)

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 H from PDB  Type:PROTEIN  Length:204
                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee........eeeeeee......eeeeeee......eee........eeee....eeeeee...hhhhheeeeeee...ee...eeeee........eeeee.....eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee......eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jo2 H   2 QSLEESGGDLVQPGASLTLTCKASGFSFGNNYDMCWVRQAPGKGLEWIGCIETGSSDSAAYATWAKGRFTISKTSSTTVTLQMTSLTAADTATYFCARNFDLWGPGTLVIVSSGQPKAPSVFPLAPCSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSVVSVTSSSQPVTCNVAHPATNTKVDKTVAP 206
                                    11        21        31    |   40        50  ||    58        68        78    ||  86        96       106       116      |132       142       152       162       172       182       192       202    
                                                            35A               52A|                            82A|                                      123|                                                                            
                                                                               52B                             82B                                       130

Chain I from PDB  Type:PROTEIN  Length:204
                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee........eeeeeee.....eeeeeeee......eee.......eeeee....eeeeee...hhhhheeeeeee...ee...eeeee........eeeee.....eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee......eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jo2 I   2 QSLEESGGDLVQPGASLTLTCKASGFSFGNNYDMCWVRQAPGKGLEWIGCIETGSSDSAAYATWAKGRFTISKTSSTTVTLQMTSLTAADTATYFCARNFDLWGPGTLVIVSSGQPKAPSVFPLAPCSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSVVSVTSSSQPVTCNVAHPATNTKVDKTVAP 206
                                    11        21        31    |   40        50  ||    58        68        78    ||  86        96       106       116      |132       142       152       162       172       182       192       202    
                                                            35A               52A|                            82A|                                      123|                                                                            
                                                                               52B                             82B                                       130

Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d4jo2l1 L:2-108 automated matches                                                                                d4jo2l2 L:109-211 automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee...hhhhh.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeee........eee...eeeeee......eeeee..........eeeeeeeeeee....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jo2 L   2 QVLTQTPSSVSTAVGSAVTINCQSSQNVYSNNNLAWFQQKPGQPPRLLIYDASKLASGVPSRFKGSGSGTQFTFTISDVQCDDAATFYCLGGYDCSSGDCAAFGGGTEVVVRGDPVAPTVLIFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSSTLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC 211
                                    11        21      ||29        39        49        59        69        79        89      |95D       105       115       125       135       145       155       165       175       185       195       205      
                                                    27A|                                                                  95A|||                                                                                                                    
                                                     27B                                                                   95B||                                                                                                                    
                                                                                                                            95C|                                                                                                                    
                                                                                                                             95D

Chain M from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d4jo2m1 M:2-108 automated matches                                                                                d4jo2m2 M:109-211 automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee...hhhhh.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeee........eee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jo2 M   2 QVLTQTPSSVSTAVGSAVTINCQSSQNVYSNNNLAWFQQKPGQPPRLLIYDASKLASGVPSRFKGSGSGTQFTFTISDVQCDDAATFYCLGGYDCSSGDCAAFGGGTEVVVRGDPVAPTVLIFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSSTLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC 211
                                    11        21      ||29        39        49        59        69        79        89      |95D       105       115       125       135       145       155       165       175       185       195       205      
                                                    27A|                                                                  95A|||                                                                                                                    
                                                     27B                                                                   95B||                                                                                                                    
                                                                                                                            95C|                                                                                                                    
                                                                                                                             95D

Chain P from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4jo2 P 303 TRKSIRIGPG 312
                                   312

Chain Q from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4jo2 Q 303 TRKSIRIGPG 312
                                   312

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Rabbit (Oryctolagus cuniculus) [TaxId: 9986] (10)

1a	d4jo2l1	L:2-108
1b	d4jo2l2	L:109-211
1c	d4jo2m1	M:2-108
1d	d4jo2m2	M:109-211

(no "CATH Domain" information available for 4JO2)

(no "Pfam Domain" information available for 4JO2)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Glu H:144 - Pro H:145	[ RasMol ]
		Glu I:144 - Pro I:145	[ RasMol ]
		Leu H:142 - Pro H:143	[ RasMol ]
		Leu I:142 - Pro I:143	[ RasMol ]
		Phe L:140 - Pro L:141	[ RasMol ]
		Phe M:140 - Pro M:141	[ RasMol ]
		Ser H:183 - Ser H:184	[ RasMol ]
		Ser H:184 - Gln H:185	[ RasMol ]
		Ser I:182 - Ser I:183	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Thr M:7 - Pro M:8	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (16, 16)

Cis Peptide Bonds (11, 11)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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